HEADER PROTEIN FIBRIL 05-AUG-22 8ANJ TITLE STRUCTURE OF THE AMYLOID-FORMING PEPTIDE DFINWL FROM HUMAN GLP-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DFINWL FROM HUMAN GLP-2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS AMYLOID, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR Z.DURVANGER REVDAT 4 04-MAR-26 8ANJ 1 REMARK REVDAT 3 19-JUN-24 8ANJ 1 REMARK REVDAT 2 09-AUG-23 8ANJ 1 JRNL REVDAT 1 02-AUG-23 8ANJ 0 JRNL AUTH D.HORVATH,Z.DURVANGER,D.K MENYHARD,M.SULYOK-EILER,F.BENCS, JRNL AUTH 2 G.GYULAI,P.HORVATH,N.TARICSKA,A.PERCZEL JRNL TITL POLYMORPHIC AMYLOID NANOSTRUCTURES OF HORMONE PEPTIDES JRNL TITL 2 INVOLVED IN GLUCOSE HOMEOSTASIS DISPLAY REVERSIBLE AMYLOID JRNL TITL 3 FORMATION. JRNL REF NAT COMMUN V. 14 4621 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37528104 JRNL DOI 10.1038/S41467-023-40294-X REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 768 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.640 REMARK 3 FREE R VALUE TEST SET COUNT : 74 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 16.9500 - 1.5500 0.98 694 74 0.1683 0.1744 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.096 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.275 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 60 REMARK 3 ANGLE : 0.956 82 REMARK 3 CHIRALITY : 0.067 8 REMARK 3 PLANARITY : 0.008 10 REMARK 3 DIHEDRAL : 8.851 18 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8ANJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1292124815. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU PHOTONJET-R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 773 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 16.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 2.880 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: CRYSTAL STRUCTURE OF LYIQWL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LYOPHILIZED PEPTIDE WAS DISSOLVED IN REMARK 280 0.6 MG/ML CONCENTRATION IN A SOLUTION CONTAINING 30 % REMARK 280 ACETONITRILE AND 0.1 % TFA AND INCUBATED AT 310K FOR 4 WEEKS., REMARK 280 EVAPORATION, RECRYSTALLIZATION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 2.43450 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 DBREF 8ANJ A 1 6 PDB 8ANJ 8ANJ 1 6 SEQRES 1 A 6 ASP PHE ILE ASN TRP LEU FORMUL 2 HOH *(H2 O) CRYST1 21.780 4.869 21.936 90.00 101.73 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.045914 0.000000 0.009533 0.00000 SCALE2 0.000000 0.205381 0.000000 0.00000 SCALE3 0.000000 0.000000 0.046559 0.00000 ATOM 1 N ASP A 1 5.737 -1.005 -0.540 1.00 19.07 N ATOM 2 CA ASP A 1 6.084 -1.772 0.706 1.00 11.92 C ATOM 3 C ASP A 1 5.735 -0.949 1.915 1.00 10.58 C ATOM 4 O ASP A 1 5.726 0.275 1.842 1.00 12.11 O ATOM 5 CB ASP A 1 7.559 -2.124 0.747 1.00 17.48 C ATOM 6 CG ASP A 1 7.948 -3.125 -0.314 1.00 21.15 C ATOM 7 OD1 ASP A 1 7.069 -3.511 -1.115 1.00 24.76 O ATOM 8 OD2 ASP A 1 9.130 -3.522 -0.322 1.00 28.48 O ATOM 9 H1 ASP A 1 6.411 -1.059 -1.119 1.00 22.89 H ATOM 10 H2 ASP A 1 5.003 -1.350 -0.906 1.00 22.89 H ATOM 11 H3 ASP A 1 5.592 -0.152 -0.332 1.00 22.89 H ATOM 12 HA ASP A 1 5.586 -2.604 0.716 1.00 14.30 H ATOM 13 HB2 ASP A 1 8.081 -1.319 0.605 1.00 20.98 H ATOM 14 HB3 ASP A 1 7.768 -2.508 1.613 1.00 20.98 H ATOM 15 N PHE A 2 5.421 -1.609 3.023 1.00 9.16 N ATOM 16 CA PHE A 2 5.097 -0.828 4.212 1.00 7.75 C ATOM 17 C PHE A 2 5.324 -1.615 5.487 1.00 7.52 C ATOM 18 O PHE A 2 5.365 -2.849 5.492 1.00 7.29 O ATOM 19 CB PHE A 2 3.649 -0.315 4.163 1.00 6.64 C ATOM 20 CG PHE A 2 2.584 -1.407 4.151 1.00 10.45 C ATOM 21 CD1 PHE A 2 2.049 -1.887 5.322 1.00 8.83 C ATOM 22 CD2 PHE A 2 2.091 -1.884 2.958 1.00 9.61 C ATOM 23 CE1 PHE A 2 1.089 -2.895 5.329 1.00 10.63 C ATOM 24 CE2 PHE A 2 1.102 -2.879 2.941 1.00 11.86 C ATOM 25 CZ PHE A 2 0.600 -3.368 4.122 1.00 10.66 C ATOM 26 H PHE A 2 5.390 -2.464 3.109 1.00 10.99 H ATOM 27 HA PHE A 2 5.715 -0.081 4.239 1.00 9.29 H ATOM 28 HB2 PHE A 2 3.492 0.238 4.944 1.00 7.97 H ATOM 29 HB3 PHE A 2 3.536 0.212 3.356 1.00 7.97 H ATOM 30 HD1 PHE A 2 2.336 -1.529 6.132 1.00 10.60 H ATOM 31 HD2 PHE A 2 2.417 -1.545 2.156 1.00 11.53 H ATOM 32 HE1 PHE A 2 0.780 -3.246 6.133 1.00 12.76 H ATOM 33 HE2 PHE A 2 0.787 -3.207 2.130 1.00 14.23 H ATOM 34 HZ PHE A 2 -0.068 -4.016 4.112 1.00 12.80 H ATOM 35 N ILE A 3 5.379 -0.857 6.581 1.00 8.81 N ATOM 36 CA ILE A 3 5.421 -1.372 7.941 1.00 9.64 C ATOM 37 C ILE A 3 4.135 -0.969 8.649 1.00 9.17 C ATOM 38 O ILE A 3 3.744 0.206 8.626 1.00 11.01 O ATOM 39 CB ILE A 3 6.648 -0.843 8.701 1.00 10.27 C ATOM 40 CG1 ILE A 3 7.924 -1.391 8.050 1.00 8.58 C ATOM 41 CG2 ILE A 3 6.558 -1.234 10.203 1.00 13.74 C ATOM 42 CD1 ILE A 3 9.241 -0.827 8.651 1.00 11.92 C ATOM 43 H ILE A 3 5.395 0.003 6.555 1.00 10.57 H ATOM 44 HA ILE A 3 5.466 -2.340 7.915 1.00 11.57 H ATOM 45 HB ILE A 3 6.671 0.125 8.651 1.00 12.32 H ATOM 46 HG12 ILE A 3 7.940 -2.354 8.161 1.00 10.30 H ATOM 47 HG13 ILE A 3 7.912 -1.166 7.107 1.00 10.30 H ATOM 48 HG21 ILE A 3 7.414 -1.064 10.625 1.00 16.49 H ATOM 49 HG22 ILE A 3 5.868 -0.700 10.627 1.00 16.49 H ATOM 50 HG23 ILE A 3 6.336 -2.176 10.271 1.00 16.49 H ATOM 51 HD11 ILE A 3 9.979 -1.056 8.065 1.00 14.30 H ATOM 52 HD12 ILE A 3 9.166 0.137 8.726 1.00 14.30 H ATOM 53 HD13 ILE A 3 9.381 -1.217 9.527 1.00 14.30 H ATOM 54 N ASN A 4 3.466 -1.947 9.256 1.00 9.67 N ATOM 55 CA ASN A 4 2.255 -1.734 10.041 1.00 8.98 C ATOM 56 C ASN A 4 2.544 -2.389 11.382 1.00 11.08 C ATOM 57 O ASN A 4 2.556 -3.620 11.485 1.00 10.21 O ATOM 58 CB ASN A 4 1.045 -2.346 9.346 1.00 9.40 C ATOM 59 CG ASN A 4 -0.224 -2.076 10.073 1.00 10.39 C ATOM 60 OD1 ASN A 4 -0.625 -0.927 10.218 1.00 13.31 O ATOM 61 ND2 ASN A 4 -0.876 -3.121 10.521 1.00 15.86 N ATOM 62 H ASN A 4 3.704 -2.773 9.226 1.00 11.61 H ATOM 63 HA ASN A 4 2.065 -0.791 10.168 1.00 10.77 H ATOM 64 HB2 ASN A 4 0.967 -1.971 8.455 1.00 11.27 H ATOM 65 HB3 ASN A 4 1.163 -3.307 9.292 1.00 11.27 H ATOM 66 HD21 ASN A 4 -1.615 -3.017 10.948 1.00 19.03 H ATOM 67 HD22 ASN A 4 -0.564 -3.912 10.388 1.00 19.03 H ATOM 68 N TRP A 5 2.832 -1.579 12.382 1.00 7.88 N ATOM 69 CA TRP A 5 3.174 -2.042 13.722 1.00 8.10 C ATOM 70 C TRP A 5 2.163 -1.468 14.702 1.00 10.83 C ATOM 71 O TRP A 5 2.076 -0.244 14.876 1.00 10.86 O ATOM 72 CB TRP A 5 4.610 -1.632 14.067 1.00 9.26 C ATOM 73 CG TRP A 5 5.166 -2.261 15.301 1.00 9.15 C ATOM 74 CD1 TRP A 5 4.608 -3.272 16.034 1.00 12.30 C ATOM 75 CD2 TRP A 5 6.413 -1.936 15.955 1.00 8.07 C ATOM 76 NE1 TRP A 5 5.417 -3.582 17.106 1.00 13.07 N ATOM 77 CE2 TRP A 5 6.541 -2.801 17.058 1.00 10.09 C ATOM 78 CE3 TRP A 5 7.432 -1.021 15.695 1.00 12.87 C ATOM 79 CZ2 TRP A 5 7.631 -2.746 17.932 1.00 12.47 C ATOM 80 CZ3 TRP A 5 8.535 -0.999 16.551 1.00 12.38 C ATOM 81 CH2 TRP A 5 8.618 -1.850 17.645 1.00 12.92 C ATOM 82 H TRP A 5 2.838 -0.722 12.312 1.00 9.46 H ATOM 83 HA TRP A 5 3.110 -3.009 13.773 1.00 9.73 H ATOM 84 HB2 TRP A 5 5.186 -1.881 13.328 1.00 11.11 H ATOM 85 HB3 TRP A 5 4.632 -0.670 14.195 1.00 11.11 H ATOM 86 HD1 TRP A 5 3.801 -3.689 15.838 1.00 14.76 H ATOM 87 HE1 TRP A 5 5.243 -4.171 17.708 1.00 15.69 H ATOM 88 HE3 TRP A 5 7.378 -0.441 14.971 1.00 15.45 H ATOM 89 HZ2 TRP A 5 7.681 -3.298 18.678 1.00 14.97 H ATOM 90 HZ3 TRP A 5 9.228 -0.401 16.384 1.00 14.86 H ATOM 91 HH2 TRP A 5 9.366 -1.808 18.197 1.00 15.50 H ATOM 92 N LEU A 6 1.371 -2.354 15.290 1.00 12.46 N ATOM 93 CA LEU A 6 0.344 -1.979 16.253 1.00 13.26 C ATOM 94 C LEU A 6 0.822 -2.288 17.659 1.00 25.94 C ATOM 95 O LEU A 6 0.355 -1.673 18.617 1.00 25.31 O ATOM 96 CB LEU A 6 -0.960 -2.730 15.991 1.00 13.29 C ATOM 97 CG LEU A 6 -1.576 -2.629 14.602 1.00 24.74 C ATOM 98 CD1 LEU A 6 -3.003 -3.149 14.647 1.00 22.71 C ATOM 99 CD2 LEU A 6 -1.512 -1.216 14.078 1.00 32.58 C ATOM 100 OXT LEU A 6 1.664 -3.173 17.860 1.00 23.17 O ATOM 101 H LEU A 6 1.409 -3.200 15.145 1.00 14.96 H ATOM 102 HA LEU A 6 0.163 -1.030 16.169 1.00 15.91 H ATOM 103 HB2 LEU A 6 -0.796 -3.672 16.155 1.00 15.94 H ATOM 104 HB3 LEU A 6 -1.623 -2.395 16.614 1.00 15.94 H ATOM 105 HG LEU A 6 -1.071 -3.175 13.979 1.00 29.68 H ATOM 106 HD11 LEU A 6 -3.185 -3.642 13.832 1.00 27.25 H ATOM 107 HD12 LEU A 6 -3.103 -3.731 15.416 1.00 27.25 H ATOM 108 HD13 LEU A 6 -3.611 -2.396 14.721 1.00 27.25 H ATOM 109 HD21 LEU A 6 -2.167 -1.112 13.370 1.00 39.10 H ATOM 110 HD22 LEU A 6 -1.708 -0.602 14.803 1.00 39.10 H ATOM 111 HD23 LEU A 6 -0.622 -1.047 13.733 1.00 39.10 H TER 112 LEU A 6 HETATM 113 O HOH A 101 4.563 -5.780 18.915 1.00 25.66 O MASTER 186 0 0 0 0 0 0 6 59 1 0 1 END