HEADER PROTEIN FIBRIL 21-AUG-24 9GJ3 TITLE STRUCTURE OF THE AMYLOID-FORMING PEPTIDE LYIQNY COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE LYIQNY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS AMYLOID, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR Z.DURVANGER REVDAT 1 09-JUL-25 9GJ3 0 JRNL AUTH F.BENCS,N.TARICSKA,Z.DURVANGER,D.HORVATH,Z.FAZEKAS, JRNL AUTH 2 V.GROLMUSZ,V.FARKAS,A.PERCZEL JRNL TITL CHEMICAL EVOLUTION OF EARLY MACROMOLECULES: FROM PREBIOTIC JRNL TITL 2 OLIGOPEPTIDES TO SELF-ORGANIZING BIOSYSTEMS VIA AMYLOID JRNL TITL 3 FORMATION. JRNL REF CHEMISTRY V. 31 04669 2025 JRNL REFN ISSN 0947-6539 JRNL PMID 40197673 JRNL DOI 10.1002/CHEM.202404669 REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 849 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.101 REMARK 3 R VALUE (WORKING SET) : 0.100 REMARK 3 FREE R VALUE : 0.110 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.250 REMARK 3 FREE R VALUE TEST SET COUNT : 87 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 21.1600 - 1.5000 1.00 762 87 0.1004 0.1097 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) : 0.000 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 5.734 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 5.41 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 : 0.012 59 REMARK 3 ANGLE : 1.387 80 REMARK 3 CHIRALITY : 0.080 8 REMARK 3 PLANARITY : 0.010 10 REMARK 3 DIHEDRAL : 16.442 21 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 9GJ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1292141093. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-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 : 849 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 21.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.490 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL 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: WATER (CONTAINING 0.1% TFA), 310K, REMARK 280 EVAPORATION, RECRYSTALLIZATION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 2.42500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.16300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 10.26900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.16300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 2.42500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 10.26900 REMARK 290 SMTRY3 4 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 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 9GJ3 A 1 6 PDB 9GJ3 9GJ3 1 6 SEQRES 1 A 6 LEU TYR ILE GLN ASN TYR CRYST1 4.850 20.538 42.326 90.00 90.00 90.00 P 21 21 21 4 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 0.206186 0.000000 0.000000 0.00000 SCALE2 0.000000 0.048690 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023626 0.00000 ATOM 1 N LEU A 1 0.383 0.195 -3.445 1.00 8.60 N ATOM 2 CA LEU A 1 0.206 -0.499 -2.144 1.00 6.61 C ATOM 3 C LEU A 1 0.946 0.302 -1.059 1.00 5.38 C ATOM 4 O LEU A 1 2.152 0.510 -1.114 1.00 4.85 O ATOM 5 CB LEU A 1 0.705 -1.933 -2.257 1.00 8.34 C ATOM 6 CG LEU A 1 0.146 -2.941 -1.269 1.00 16.62 C ATOM 7 CD1 LEU A 1 0.550 -4.334 -1.706 1.00 18.61 C ATOM 8 CD2 LEU A 1 0.706 -2.664 0.060 1.00 17.26 C ATOM 9 H1 LEU A 1 0.815 -0.340 -4.011 1.00 10.33 H ATOM 10 H2 LEU A 1 -0.414 0.402 -3.783 1.00 10.33 H ATOM 11 H3 LEU A 1 0.855 0.940 -3.323 1.00 10.33 H ATOM 12 HA LEU A 1 -0.726 -0.558 -1.884 1.00 7.93 H ATOM 13 HB2 LEU A 1 0.484 -2.255 -3.144 1.00 10.01 H ATOM 14 HB3 LEU A 1 1.667 -1.924 -2.136 1.00 10.01 H ATOM 15 HG LEU A 1 -0.822 -2.884 -1.230 1.00 19.95 H ATOM 16 HD11 LEU A 1 0.200 -4.978 -1.071 1.00 22.34 H ATOM 17 HD12 LEU A 1 0.183 -4.506 -2.588 1.00 22.34 H ATOM 18 HD13 LEU A 1 1.518 -4.388 -1.734 1.00 22.34 H ATOM 19 HD21 LEU A 1 0.575 -3.440 0.626 1.00 20.72 H ATOM 20 HD22 LEU A 1 1.653 -2.476 -0.029 1.00 20.72 H ATOM 21 HD23 LEU A 1 0.251 -1.896 0.441 1.00 20.72 H ATOM 22 N TYR A 2 0.182 0.768 -0.074 1.00 4.29 N ATOM 23 CA TYR A 2 0.685 1.580 1.030 1.00 3.09 C ATOM 24 C TYR A 2 0.066 1.033 2.303 1.00 5.25 C ATOM 25 O TYR A 2 -1.165 0.936 2.397 1.00 3.57 O ATOM 26 CB TYR A 2 0.265 3.037 0.866 1.00 3.34 C ATOM 27 CG TYR A 2 0.947 4.116 1.665 1.00 2.15 C ATOM 28 CD1 TYR A 2 1.965 3.849 2.553 1.00 2.58 C ATOM 29 CD2 TYR A 2 0.556 5.427 1.507 1.00 3.28 C ATOM 30 CE1 TYR A 2 2.602 4.882 3.249 1.00 4.15 C ATOM 31 CE2 TYR A 2 1.197 6.464 2.172 1.00 2.90 C ATOM 32 CZ TYR A 2 2.199 6.192 3.048 1.00 2.79 C ATOM 33 OH TYR A 2 2.870 7.222 3.682 1.00 6.16 O ATOM 34 H TYR A 2 -0.664 0.622 -0.021 1.00 5.15 H ATOM 35 HA TYR A 2 1.653 1.533 1.075 1.00 3.71 H ATOM 36 HB2 TYR A 2 0.397 3.271 -0.066 1.00 4.01 H ATOM 37 HB3 TYR A 2 -0.677 3.091 1.091 1.00 4.01 H ATOM 38 HD1 TYR A 2 2.233 2.969 2.693 1.00 3.10 H ATOM 39 HD2 TYR A 2 -0.155 5.623 0.941 1.00 3.94 H ATOM 40 HE1 TYR A 2 3.292 4.690 3.842 1.00 4.98 H ATOM 41 HE2 TYR A 2 0.941 7.345 2.017 1.00 3.48 H ATOM 42 HH TYR A 2 2.415 7.926 3.647 1.00 7.40 H ATOM 43 N ILE A 3 0.897 0.677 3.272 1.00 3.90 N ATOM 44 CA ILE A 3 0.439 0.257 4.596 1.00 2.40 C ATOM 45 C ILE A 3 1.021 1.208 5.620 1.00 3.15 C ATOM 46 O ILE A 3 2.246 1.369 5.693 1.00 3.15 O ATOM 47 CB ILE A 3 0.856 -1.184 4.938 1.00 1.80 C ATOM 48 CG1 ILE A 3 0.220 -2.166 3.958 1.00 5.18 C ATOM 49 CG2 ILE A 3 0.437 -1.537 6.384 1.00 3.98 C ATOM 50 CD1 ILE A 3 0.815 -3.567 4.042 1.00 7.25 C ATOM 51 H ILE A 3 1.753 0.670 3.188 1.00 4.69 H ATOM 52 HA ILE A 3 -0.529 0.314 4.614 1.00 2.89 H ATOM 53 HB ILE A 3 1.822 -1.247 4.864 1.00 2.16 H ATOM 54 HG12 ILE A 3 -0.728 -2.232 4.151 1.00 6.22 H ATOM 55 HG13 ILE A 3 0.353 -1.839 3.054 1.00 6.22 H ATOM 56 HG21 ILE A 3 0.501 -2.497 6.506 1.00 4.78 H ATOM 57 HG22 ILE A 3 1.030 -1.084 7.004 1.00 4.78 H ATOM 58 HG23 ILE A 3 -0.477 -1.245 6.527 1.00 4.78 H ATOM 59 HD11 ILE A 3 0.597 -4.052 3.230 1.00 8.70 H ATOM 60 HD12 ILE A 3 1.778 -3.497 4.135 1.00 8.70 H ATOM 61 HD13 ILE A 3 0.441 -4.024 4.811 1.00 8.70 H ATOM 62 N GLN A 4 0.162 1.817 6.438 1.00 2.92 N ATOM 63 CA GLN A 4 0.575 2.594 7.602 1.00 2.07 C ATOM 64 C GLN A 4 -0.031 1.900 8.816 1.00 3.78 C ATOM 65 O GLN A 4 -1.262 1.839 8.948 1.00 5.18 O ATOM 66 CB GLN A 4 0.134 4.053 7.513 1.00 3.81 C ATOM 67 CG GLN A 4 0.791 4.748 6.321 1.00 2.43 C ATOM 68 CD GLN A 4 0.419 6.217 6.183 1.00 5.23 C ATOM 69 OE1 GLN A 4 1.276 7.118 6.202 1.00 8.54 O ATOM 70 NE2 GLN A 4 -0.847 6.464 6.025 1.00 2.92 N ATOM 71 H GLN A 4 -0.692 1.792 6.334 1.00 3.51 H ATOM 72 HA GLN A 4 1.543 2.601 7.672 1.00 2.49 H ATOM 73 HB2 GLN A 4 -0.829 4.094 7.401 1.00 4.57 H ATOM 74 HB3 GLN A 4 0.394 4.520 8.323 1.00 4.57 H ATOM 75 HG2 GLN A 4 1.754 4.696 6.422 1.00 2.92 H ATOM 76 HG3 GLN A 4 0.518 4.296 5.508 1.00 2.92 H ATOM 77 HE21 GLN A 4 -1.412 5.817 6.005 1.00 3.50 H ATOM 78 HE22 GLN A 4 -1.119 7.276 5.941 1.00 3.50 H ATOM 79 N ASN A 5 0.824 1.365 9.686 1.00 2.88 N ATOM 80 CA ASN A 5 0.404 0.499 10.779 1.00 2.54 C ATOM 81 C ASN A 5 0.847 1.055 12.123 1.00 4.77 C ATOM 82 O ASN A 5 2.028 1.347 12.341 1.00 5.55 O ATOM 83 CB ASN A 5 0.975 -0.899 10.594 1.00 4.66 C ATOM 84 CG ASN A 5 0.540 -1.836 11.667 1.00 7.08 C ATOM 85 OD1 ASN A 5 -0.586 -2.291 11.687 1.00 5.78 O ATOM 86 ND2 ASN A 5 1.441 -2.105 12.598 1.00 8.88 N ATOM 87 H ASN A 5 1.674 1.494 9.660 1.00 3.46 H ATOM 88 HA ASN A 5 -0.565 0.463 10.788 1.00 3.05 H ATOM 89 HB2 ASN A 5 0.676 -1.255 9.743 1.00 5.59 H ATOM 90 HB3 ASN A 5 1.944 -0.851 10.611 1.00 5.59 H ATOM 91 HD21 ASN A 5 1.246 -2.639 13.243 1.00 10.66 H ATOM 92 HD22 ASN A 5 2.221 -1.745 12.558 1.00 10.66 H ATOM 93 N TYR A 6 -0.119 1.199 13.020 1.00 3.89 N ATOM 94 CA TYR A 6 0.112 1.584 14.397 1.00 3.44 C ATOM 95 C TYR A 6 -0.542 0.560 15.327 1.00 8.02 C ATOM 96 O TYR A 6 -1.331 -0.311 14.902 1.00 9.70 O ATOM 97 CB TYR A 6 -0.485 2.963 14.694 1.00 5.06 C ATOM 98 CG TYR A 6 0.102 4.105 13.913 1.00 3.88 C ATOM 99 CD1 TYR A 6 -0.364 4.417 12.641 1.00 4.41 C ATOM 100 CD2 TYR A 6 1.099 4.880 14.451 1.00 3.63 C ATOM 101 CE1 TYR A 6 0.172 5.468 11.918 1.00 4.92 C ATOM 102 CE2 TYR A 6 1.656 5.923 13.730 1.00 5.88 C ATOM 103 CZ TYR A 6 1.182 6.222 12.474 1.00 3.97 C ATOM 104 OH TYR A 6 1.763 7.292 11.816 1.00 7.66 O ATOM 105 OXT TYR A 6 -0.328 0.665 16.536 1.00 9.62 O ATOM 106 H TYR A 6 -0.952 1.073 12.845 1.00 4.67 H ATOM 107 HA TYR A 6 1.067 1.628 14.558 1.00 4.13 H ATOM 108 HB2 TYR A 6 -1.434 2.935 14.495 1.00 6.07 H ATOM 109 HB3 TYR A 6 -0.350 3.158 15.635 1.00 6.07 H ATOM 110 HD1 TYR A 6 -1.050 3.910 12.269 1.00 5.30 H ATOM 111 HD2 TYR A 6 1.405 4.702 15.311 1.00 4.37 H ATOM 112 HE1 TYR A 6 -0.146 5.663 11.066 1.00 5.91 H ATOM 113 HE2 TYR A 6 2.351 6.422 14.095 1.00 7.05 H ATOM 114 HH TYR A 6 1.557 7.275 11.001 1.00 9.20 H TER 115 TYR A 6 MASTER 187 0 0 0 0 0 0 6 58 1 0 1 END