HEADER PROTEIN FIBRIL 18-AUG-21 7RVI
TITLE SEGMENT FROM NAKED MOLE RAT (ELK T174S) PRION PROTEIN 168-176
TITLE 2 QYNNQNSFV
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: MAJOR PRION PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 158-166;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: HETEROCEPHALUS GLABER;
SOURCE 4 ORGANISM_COMMON: NAKED MOLE RAT;
SOURCE 5 ORGANISM_TAXID: 10181
KEYWDS AMYLOID, PRION, FIBRIL, NAKED MOLE RAT, PROTEIN FIBRIL
EXPDTA ELECTRON CRYSTALLOGRAPHY
AUTHOR C.GLYNN,J.A.RODRIGUEZ,E.HERNANDEZ
REVDAT 2 22-MAY-24 7RVI 1 REMARK
REVDAT 1 24-AUG-22 7RVI 0
JRNL AUTH C.GLYNN,E.HERNANDEZ,M.GALLAGHER-JONES,J.MIAO,J.A.RODRIGUEZ
JRNL TITL STRUCTURAL AND BIOPHYSICAL CONSEQUENCES OF SEQUENCE
JRNL TITL 2 VARIATION IN THE B2A2 LOOP OF MAMMALIAN PRIONS
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.05 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.19.2_4158
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) : 1.05
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.76
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380
REMARK 3 COMPLETENESS FOR RANGE (%) : 80.2
REMARK 3 NUMBER OF REFLECTIONS : 2612
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.227
REMARK 3 R VALUE (WORKING SET) : 0.222
REMARK 3 FREE R VALUE : 0.265
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030
REMARK 3 FREE R VALUE TEST SET COUNT : 262
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 10.7600 - 1.3200 0.78 1189 133 0.2280 0.2655
REMARK 3 2 1.3200 - 1.0500 0.82 1161 129 0.2119 0.2638
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) : 0.130
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.670
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 2.75
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 3.94
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 7RVI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-AUG-21.
REMARK 100 THE DEPOSITION ID IS D_1000259066.
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 : 28-JUN-18
REMARK 240 TEMPERATURE (KELVIN) : 100.0
REMARK 240 PH : 6.50
REMARK 240 NUMBER OF CRYSTALS USED : 1
REMARK 240 MICROSCOPE MODEL : FEI TECNAI F30
REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K)
REMARK 240 ACCELERATION VOLTAGE (KV) : 300
REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 2612
REMARK 240 RESOLUTION RANGE HIGH (A) : 1.050
REMARK 240 RESOLUTION RANGE LOW (A) : 10.760
REMARK 240 DATA SCALING SOFTWARE : XSCALE
REMARK 240 COMPLETENESS FOR RANGE (%) : 79.9
REMARK 240 DATA REDUNDANCY : 8.391
REMARK 240 IN THE HIGHEST RESOLUTION SHELL
REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.05
REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.08
REMARK 240 COMPLETENESS FOR SHELL (%) : 83.5
REMARK 240 DATA REDUNDANCY IN SHELL : 8.56
REMARK 240 R MERGE FOR SHELL (I) : 0.58900
REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING
REMARK 240 SOFTWARE USED : SHELXD
REMARK 240 STARTING MODEL : NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
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 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 31.38000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 2.42500
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 31.38000
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 2.42500
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
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 202 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 VAL A 176 O
REMARK 620 2 VAL A 176 OXT 53.8
REMARK 620 3 CAC A 201 O2 17.5 71.1
REMARK 620 4 CAC A 201 O1 16.0 69.8 3.7
REMARK 620 N 1 2 3
DBREF 7RVI A 168 176 UNP G5B4V6 G5B4V6_HETGA 158 166
SEQRES 1 A 9 GLN TYR ASN ASN GLN ASN SER PHE VAL
HET CAC A 201 5
HET NA A 202 1
HETNAM CAC CACODYLATE ION
HETNAM NA SODIUM ION
HETSYN CAC DIMETHYLARSINATE
FORMUL 2 CAC C2 H6 AS O2 1-
FORMUL 3 NA NA 1+
FORMUL 4 HOH *3(H2 O)
LINK O VAL A 176 NA NA A 202 1555 3454 2.06
LINK OXT VAL A 176 NA NA A 202 1555 3454 2.53
LINK O2 CAC A 201 NA NA A 202 1555 1555 1.98
LINK O1 CAC A 201 NA NA A 202 1555 1545 2.07
CRYST1 62.760 4.850 21.520 90.00 109.14 90.00 C 1 2 1 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 0.015934 0.000000 0.005530 0.00000
SCALE2 0.000000 0.206186 0.000000 0.00000
SCALE3 0.000000 0.000000 0.049187 0.00000
ATOM 1 N GLN A 168 17.842 0.513 22.871 1.00 4.46 N
ATOM 2 CA GLN A 168 16.631 -0.238 22.598 1.00 2.31 C
ATOM 3 C GLN A 168 16.092 0.196 21.238 1.00 2.11 C
ATOM 4 O GLN A 168 16.200 1.361 20.898 1.00 4.13 O
ATOM 5 CB GLN A 168 15.611 0.023 23.698 1.00 2.31 C
ATOM 6 CG GLN A 168 16.037 -0.549 25.088 1.00 3.97 C
ATOM 7 CD GLN A 168 15.235 0.018 26.254 1.00 1.62 C
ATOM 8 OE1 GLN A 168 14.924 1.203 26.276 1.00 7.17 O
ATOM 9 NE2 GLN A 168 14.876 -0.820 27.209 1.00 4.78 N
ATOM 10 N TYR A 169 15.547 -0.739 20.454 1.00 2.99 N
ATOM 11 CA TYR A 169 15.101 -0.464 19.084 1.00 1.87 C
ATOM 12 C TYR A 169 13.641 -0.897 18.912 1.00 2.35 C
ATOM 13 O TYR A 169 13.309 -2.069 19.115 1.00 1.36 O
ATOM 14 CB TYR A 169 15.998 -1.173 18.060 1.00 2.29 C
ATOM 15 CG TYR A 169 15.552 -1.018 16.600 1.00 3.26 C
ATOM 16 CD1 TYR A 169 14.527 -1.812 16.059 1.00 3.02 C
ATOM 17 CD2 TYR A 169 16.195 -0.107 15.758 1.00 3.05 C
ATOM 18 CE1 TYR A 169 14.139 -1.661 14.718 1.00 2.87 C
ATOM 19 CE2 TYR A 169 15.808 0.048 14.422 1.00 4.03 C
ATOM 20 CZ TYR A 169 14.784 -0.738 13.915 1.00 3.38 C
ATOM 21 OH TYR A 169 14.392 -0.625 12.595 1.00 4.64 O
ATOM 22 N ASN A 170 12.772 0.046 18.537 1.00 2.30 N
ATOM 23 CA ASN A 170 11.395 -0.281 18.200 1.00 2.30 C
ATOM 24 C ASN A 170 11.040 0.318 16.850 1.00 1.45 C
ATOM 25 O ASN A 170 11.219 1.522 16.657 1.00 4.86 O
ATOM 26 CB ASN A 170 10.422 0.322 19.206 1.00 1.41 C
ATOM 27 CG ASN A 170 8.995 0.104 18.808 1.00 1.64 C
ATOM 28 OD1 ASN A 170 8.502 -1.036 18.809 1.00 4.30 O
ATOM 29 ND2 ASN A 170 8.315 1.176 18.441 1.00 3.45 N
ATOM 30 N ASN A 171 10.498 -0.497 15.946 1.00 1.30 N
ATOM 31 CA ASN A 171 9.964 -0.016 14.675 1.00 1.51 C
ATOM 32 C ASN A 171 8.636 -0.730 14.474 1.00 1.36 C
ATOM 33 O ASN A 171 8.624 -1.951 14.295 1.00 3.08 O
ATOM 34 CB ASN A 171 10.943 -0.274 13.510 1.00 2.60 C
ATOM 35 CG ASN A 171 10.350 0.016 12.122 1.00 2.23 C
ATOM 36 OD1 ASN A 171 10.697 -0.669 11.149 1.00 3.16 O
ATOM 37 ND2 ASN A 171 9.495 1.028 12.031 1.00 3.65 N
ATOM 38 N GLN A 172 7.534 0.017 14.574 1.00 2.22 N
ATOM 39 CA GLN A 172 6.193 -0.483 14.296 1.00 0.75 C
ATOM 40 C GLN A 172 5.683 0.138 12.995 1.00 1.14 C
ATOM 41 O GLN A 172 5.551 1.362 12.893 1.00 3.04 O
ATOM 42 CB GLN A 172 5.259 -0.161 15.458 1.00 0.80 C
ATOM 43 CG GLN A 172 5.574 -0.903 16.749 1.00 1.80 C
ATOM 44 CD GLN A 172 5.027 -0.243 17.970 1.00 1.32 C
ATOM 45 OE1 GLN A 172 5.161 0.968 18.134 1.00 3.51 O
ATOM 46 NE2 GLN A 172 4.439 -1.030 18.861 1.00 4.73 N
ATOM 47 N ASN A 173 5.360 -0.711 12.023 1.00 2.56 N
ATOM 48 CA ASN A 173 4.872 -0.253 10.731 1.00 1.60 C
ATOM 49 C ASN A 173 3.482 -0.812 10.465 1.00 1.89 C
ATOM 50 O ASN A 173 3.237 -2.005 10.676 1.00 4.67 O
ATOM 51 CB ASN A 173 5.746 -0.748 9.601 1.00 2.10 C
ATOM 52 CG ASN A 173 7.145 -0.230 9.672 1.00 2.38 C
ATOM 53 OD1 ASN A 173 7.364 0.949 9.922 1.00 4.45 O
ATOM 54 ND2 ASN A 173 8.098 -1.092 9.390 1.00 2.93 N
ATOM 55 N SER A 174 2.607 0.042 9.940 1.00 1.44 N
ATOM 56 CA SER A 174 1.264 -0.337 9.532 1.00 1.91 C
ATOM 57 C SER A 174 0.984 0.207 8.137 1.00 1.83 C
ATOM 58 O SER A 174 1.116 1.409 7.892 1.00 4.73 O
ATOM 59 CB SER A 174 0.237 0.190 10.528 1.00 2.50 C
ATOM 60 OG SER A 174 -1.075 -0.035 10.083 1.00 4.00 O
ATOM 61 N PHE A 175 0.578 -0.685 7.240 1.00 2.90 N
ATOM 62 CA PHE A 175 0.228 -0.342 5.869 1.00 2.94 C
ATOM 63 C PHE A 175 -1.180 -0.848 5.632 1.00 3.22 C
ATOM 64 O PHE A 175 -1.427 -2.053 5.740 1.00 7.23 O
ATOM 65 CB PHE A 175 1.164 -0.993 4.866 1.00 2.82 C
ATOM 66 CG PHE A 175 2.595 -0.647 5.056 1.00 3.63 C
ATOM 67 CD1 PHE A 175 3.385 -1.393 5.903 1.00 4.60 C
ATOM 68 CD2 PHE A 175 3.154 0.436 4.395 1.00 4.64 C
ATOM 69 CE1 PHE A 175 4.703 -1.082 6.082 1.00 4.94 C
ATOM 70 CE2 PHE A 175 4.494 0.748 4.555 1.00 4.38 C
ATOM 71 CZ PHE A 175 5.265 -0.008 5.405 1.00 5.41 C
ATOM 72 N VAL A 176 -2.096 0.067 5.331 1.00 4.71 N
ATOM 73 CA VAL A 176 -3.518 -0.212 5.303 1.00 4.08 C
ATOM 74 C VAL A 176 -4.130 0.489 4.093 1.00 4.05 C
ATOM 75 O VAL A 176 -3.437 1.291 3.450 1.00 7.38 O
ATOM 76 CB VAL A 176 -4.173 0.295 6.623 1.00 7.96 C
ATOM 77 CG1 VAL A 176 -5.641 -0.004 6.675 1.00 7.18 C
ATOM 78 CG2 VAL A 176 -3.484 -0.283 7.825 1.00 8.53 C
ATOM 79 OXT VAL A 176 -5.297 0.318 3.742 1.00 5.43 O
TER 80 VAL A 176
HETATM 81 AS CAC A 201 20.304 -2.789 20.224 1.00 12.92 AS
HETATM 82 O1 CAC A 201 20.928 -3.940 21.359 1.00 8.76 O
HETATM 83 O2 CAC A 201 19.123 -1.728 20.913 1.00 11.70 O
HETATM 84 C1 CAC A 201 19.410 -3.708 18.737 1.00 8.84 C
HETATM 85 C2 CAC A 201 21.808 -1.781 19.463 1.00 10.88 C
HETATM 86 NA NA A 202 19.650 -0.413 22.300 1.00 3.69 NA
HETATM 87 O HOH A 301 12.858 -2.431 11.575 1.00 6.19 O
HETATM 88 O HOH A 302 -1.881 2.328 8.993 1.00 11.78 O
HETATM 89 O HOH A 303 -0.756 1.141 2.581 1.00 9.05 O
CONECT 81 82 83 84 85
CONECT 82 81
CONECT 83 81 86
CONECT 84 81
CONECT 85 81
CONECT 86 83
MASTER 173 0 2 0 0 0 0 6 88 1 6 1
END