HEADER PROTEIN FIBRIL 29-MAY-21 7N2J TITLE MICROED STRUCTURE OF A MUTANT MAMMALIAN PRION SEGMENT PHASED BY TITLE 2 ARCIMBOLDO-BORGES COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRION PROTEIN; 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 PRION, MICROED, AMYLOID, PROTEIN FIBRIL EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR L.S.RICHARDS,M.D.FLORES,C.T.ZEE,C.GLYNN,M.GALLAGHER-JONES,M.R.SAWAYA REVDAT 3 22-MAY-24 7N2J 1 REMARK REVDAT 2 10-MAY-23 7N2J 1 JRNL REVDAT 1 01-JUN-22 7N2J 0 JRNL AUTH L.S.RICHARDS,M.D.FLORES,C.MILLAN,C.GLYNN,C.T.ZEE,M.R.SAWAYA, JRNL AUTH 2 M.GALLAGHER-JONES,R.J.BORGES,I.USON,J.A.RODRIGUEZ JRNL TITL FRAGMENT-BASED AB INITIO PHASING OF PEPTIDIC NANOCRYSTALS BY JRNL TITL 2 MICROED. JRNL REF ACS BIO MED CHEM AU V. 3 201 2023 JRNL REFN ESSN 2694-2437 JRNL PMID 37096030 JRNL DOI 10.1021/ACSBIOMEDCHEMAU.2C00082 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.240 REMARK 3 COMPLETENESS FOR RANGE (%) : 80.4 REMARK 3 NUMBER OF REFLECTIONS : 730 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.040 REMARK 3 FREE R VALUE TEST SET COUNT : 66 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 7.9800 - 3.1707 0.80 67 7 0.1345 0.1855 REMARK 3 2 3.1707 - 2.5434 0.80 51 5 0.2068 0.2019 REMARK 3 3 2.5434 - 2.2300 0.85 84 8 0.1603 0.1674 REMARK 3 4 2.2300 - 2.0297 0.78 62 7 0.1492 0.1924 REMARK 3 5 2.0297 - 1.8863 0.81 74 7 0.1591 0.3424 REMARK 3 6 1.8863 - 1.7764 0.80 59 6 0.2183 0.4625 REMARK 3 7 1.7764 - 1.6883 0.79 56 5 0.2150 0.3783 REMARK 3 8 1.6883 - 1.6155 0.86 64 7 0.2121 0.2802 REMARK 3 9 1.6155 - 1.5537 0.79 78 7 0.1859 0.1276 REMARK 3 10 1.5537 - 1.5005 0.81 69 7 0.2290 0.1879 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) : 24.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 4.56 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7N2J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1000254652. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : NULL REMARK 240 TEMPERATURE (KELVIN) : NULL REMARK 240 PH : NULL REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : FEI TALOS ARCTICA REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 915 REMARK 240 RESOLUTION RANGE HIGH (A) : 0.900 REMARK 240 RESOLUTION RANGE LOW (A) : 7.980 REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 81.0 REMARK 240 DATA REDUNDANCY : 5.383 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :0.90 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :0.92 REMARK 240 COMPLETENESS FOR SHELL (%) : 81.1 REMARK 240 DATA REDUNDANCY IN SHELL : 4.78 REMARK 240 R MERGE FOR SHELL (I) : 0.46600 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 240 SOFTWARE USED : NULL REMARK 240 STARTING MODEL : NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 1380 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 7N2J A -1 7 PDB 7N2J 7N2J -1 7 SEQRES 1 A 9 GLN TYR ASN ASN GLU ASN ASN PHE VAL FORMUL 2 HOH *(H2 O) CRYST1 4.870 10.060 30.660 94.85 90.26 99.99 P 1 1 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 0.205339 0.036162 0.004095 0.00000 SCALE2 0.000000 0.100933 0.008780 0.00000 SCALE3 0.000000 0.000000 0.032739 0.00000 ATOM 1 N GLN A -1 -0.029 -6.868 -4.770 1.00 6.62 N ATOM 2 CA GLN A -1 0.488 -5.893 -3.826 1.00 3.95 C ATOM 3 C GLN A -1 -0.178 -5.999 -2.457 1.00 5.01 C ATOM 4 O GLN A -1 -1.403 -6.045 -2.357 1.00 7.77 O ATOM 5 CB GLN A -1 0.310 -4.483 -4.391 1.00 6.79 C ATOM 6 CG GLN A -1 1.099 -3.411 -3.683 1.00 6.21 C ATOM 7 CD GLN A -1 0.738 -2.052 -4.207 1.00 5.72 C ATOM 8 OE1 GLN A -1 -0.407 -1.611 -4.080 1.00 8.20 O ATOM 9 NE2 GLN A -1 1.702 -1.381 -4.820 1.00 8.87 N ATOM 10 N TYR A 0 0.642 -6.004 -1.409 1.00 1.70 N ATOM 11 CA TYR A 0 0.201 -6.154 -0.026 1.00 1.71 C ATOM 12 C TYR A 0 0.629 -4.917 0.756 1.00 2.21 C ATOM 13 O TYR A 0 1.818 -4.596 0.797 1.00 1.96 O ATOM 14 CB TYR A 0 0.814 -7.433 0.560 1.00 2.07 C ATOM 15 CG TYR A 0 0.452 -7.785 1.983 1.00 1.44 C ATOM 16 CD1 TYR A 0 -0.557 -8.713 2.248 1.00 0.92 C ATOM 17 CD2 TYR A 0 1.156 -7.244 3.061 1.00 1.07 C ATOM 18 CE1 TYR A 0 -0.884 -9.071 3.545 1.00 0.52 C ATOM 19 CE2 TYR A 0 0.833 -7.595 4.371 1.00 1.68 C ATOM 20 CZ TYR A 0 -0.184 -8.517 4.600 1.00 0.00 C ATOM 21 OH TYR A 0 -0.520 -8.883 5.887 1.00 1.06 O ATOM 22 N ASN A 1 -0.335 -4.216 1.363 1.00 2.98 N ATOM 23 CA ASN A 1 -0.068 -2.956 2.062 1.00 1.63 C ATOM 24 C ASN A 1 -0.647 -3.029 3.469 1.00 1.09 C ATOM 25 O ASN A 1 -1.854 -3.234 3.632 1.00 1.37 O ATOM 26 CB ASN A 1 -0.660 -1.751 1.317 1.00 0.93 C ATOM 27 CG ASN A 1 -0.173 -1.646 -0.108 1.00 3.14 C ATOM 28 OD1 ASN A 1 1.014 -1.473 -0.357 1.00 5.15 O ATOM 29 ND2 ASN A 1 -1.097 -1.752 -1.058 1.00 5.80 N ATOM 30 N ASN A 2 0.200 -2.827 4.479 1.00 0.73 N ATOM 31 CA ASN A 2 -0.240 -2.965 5.862 1.00 1.09 C ATOM 32 C ASN A 2 0.515 -1.982 6.744 1.00 1.36 C ATOM 33 O ASN A 2 1.532 -1.402 6.346 1.00 0.66 O ATOM 34 CB ASN A 2 -0.050 -4.408 6.372 1.00 0.20 C ATOM 35 CG ASN A 2 -1.231 -4.894 7.170 1.00 1.68 C ATOM 36 OD1 ASN A 2 -1.835 -4.131 7.916 1.00 2.63 O ATOM 37 ND2 ASN A 2 -1.593 -6.167 6.995 1.00 0.58 N ATOM 38 N GLU A 3 -0.015 -1.790 7.952 1.00 0.42 N ATOM 39 CA GLU A 3 0.660 -1.014 8.979 1.00 1.39 C ATOM 40 C GLU A 3 0.224 -1.542 10.333 1.00 0.36 C ATOM 41 O GLU A 3 -0.915 -1.980 10.496 1.00 1.40 O ATOM 42 CB GLU A 3 0.354 0.484 8.855 1.00 1.06 C ATOM 43 CG GLU A 3 -1.086 0.862 9.210 1.00 2.06 C ATOM 44 CD GLU A 3 -1.277 2.358 9.448 1.00 4.03 C ATOM 45 OE1 GLU A 3 -0.695 3.169 8.700 1.00 4.66 O ATOM 46 OE2 GLU A 3 -2.012 2.730 10.387 1.00 1.92 O ATOM 47 N ASN A 4 1.146 -1.530 11.295 1.00 1.13 N ATOM 48 CA ASN A 4 0.857 -2.053 12.627 1.00 2.58 C ATOM 49 C ASN A 4 1.530 -1.173 13.666 1.00 3.03 C ATOM 50 O ASN A 4 2.761 -1.062 13.683 1.00 2.41 O ATOM 51 CB ASN A 4 1.322 -3.515 12.772 1.00 1.31 C ATOM 52 CG ASN A 4 0.867 -4.389 11.621 1.00 1.33 C ATOM 53 OD1 ASN A 4 -0.276 -4.830 11.587 1.00 3.79 O ATOM 54 ND2 ASN A 4 1.763 -4.641 10.665 1.00 2.52 N ATOM 55 N ASN A 5 0.731 -0.554 14.533 1.00 3.27 N ATOM 56 CA ASN A 5 1.241 0.307 15.590 1.00 4.40 C ATOM 57 C ASN A 5 0.714 -0.190 16.923 1.00 4.49 C ATOM 58 O ASN A 5 -0.493 -0.375 17.081 1.00 3.51 O ATOM 59 CB ASN A 5 0.833 1.767 15.365 1.00 4.65 C ATOM 60 CG ASN A 5 1.388 2.336 14.067 1.00 5.43 C ATOM 61 OD1 ASN A 5 0.641 2.773 13.189 1.00 8.31 O ATOM 62 ND2 ASN A 5 2.706 2.320 13.938 1.00 4.91 N ATOM 63 N PHE A 6 1.614 -0.384 17.884 1.00 3.36 N ATOM 64 CA PHE A 6 1.255 -0.881 19.210 1.00 5.58 C ATOM 65 C PHE A 6 1.720 0.137 20.244 1.00 6.45 C ATOM 66 O PHE A 6 2.923 0.372 20.391 1.00 6.07 O ATOM 67 CB PHE A 6 1.878 -2.254 19.468 1.00 5.37 C ATOM 68 CG PHE A 6 1.501 -3.304 18.442 1.00 6.63 C ATOM 69 CD1 PHE A 6 0.465 -4.192 18.679 1.00 6.87 C ATOM 70 CD2 PHE A 6 2.198 -3.410 17.246 1.00 5.24 C ATOM 71 CE1 PHE A 6 0.128 -5.165 17.743 1.00 5.21 C ATOM 72 CE2 PHE A 6 1.853 -4.375 16.308 1.00 9.54 C ATOM 73 CZ PHE A 6 0.813 -5.251 16.561 1.00 4.25 C ATOM 74 N VAL A 7 0.773 0.755 20.944 1.00 8.45 N ATOM 75 CA VAL A 7 1.100 1.743 21.972 1.00 10.91 C ATOM 76 C VAL A 7 0.351 1.433 23.258 1.00 21.56 C ATOM 77 O VAL A 7 0.776 1.873 24.325 1.00 23.19 O ATOM 78 CB VAL A 7 0.785 3.176 21.515 1.00 12.52 C ATOM 79 CG1 VAL A 7 1.553 4.178 22.363 1.00 14.42 C ATOM 80 CG2 VAL A 7 1.124 3.352 20.052 1.00 14.63 C ATOM 81 OXT VAL A 7 -0.682 0.753 23.262 1.00 16.75 O TER 82 VAL A 7 HETATM 83 O HOH A 101 1.310 0.962 -1.663 1.00 5.73 O MASTER 161 0 0 0 0 0 0 6 82 1 0 1 END