HEADER PROTEIN FIBRIL 18-AUG-21 7RVG TITLE SEGMENT FROM RABBIT/PIG PRION PROTEIN 168-176 QYSNQNSFV COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR PRION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 167-175; COMPND 5 SYNONYM: PRP,PRP27-30,PRP33-35C; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: ALSO SUS SCROFA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 4 ORGANISM_COMMON: RABBIT; SOURCE 5 ORGANISM_TAXID: 9986 KEYWDS AMYLOID, PRION, FIBRIL, RABBIT, PIG, PROTEIN FIBRIL EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR C.GLYNN,J.A.RODRIGUEZ,E.HERNANDEZ REVDAT 2 22-MAY-24 7RVG 1 REMARK REVDAT 1 24-AUG-22 7RVG 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. 1.00 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) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 74.8 REMARK 3 NUMBER OF REFLECTIONS : 2658 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.890 REMARK 3 FREE R VALUE TEST SET COUNT : 263 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 7.1800 - 1.2600 0.74 1207 133 0.1980 0.1911 REMARK 3 2 1.2600 - 1.0000 0.76 1188 130 0.2586 0.2773 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 4.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 5.57 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 7RVG 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_1000259070. 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 : 22-MAR-17 REMARK 240 TEMPERATURE (KELVIN) : 100.0 REMARK 240 PH : 9.00 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 : 2680 REMARK 240 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 240 RESOLUTION RANGE LOW (A) : 7.180 REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 74.9 REMARK 240 DATA REDUNDANCY : 7.375 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.00 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.03 REMARK 240 COMPLETENESS FOR SHELL (%) : 71.7 REMARK 240 DATA REDUNDANCY IN SHELL : 6.63 REMARK 240 R MERGE FOR SHELL (I) : 0.69800 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: 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 2.43000 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 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 7RVG A 168 176 UNP Q95211 PRIO_RABIT 167 175 SEQRES 1 A 9 GLN TYR SER ASN GLN ASN SER PHE VAL FORMUL 2 HOH *4(H2 O) CRYST1 23.570 4.860 27.700 90.00 111.21 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 0.042427 0.000000 0.016463 0.00000 SCALE2 0.000000 0.205761 0.000000 0.00000 SCALE3 0.000000 0.000000 0.038724 0.00000 ANISOU 1 N GLN A 168 902 1075 690 -203 -382 -178 N ANISOU 2 CA GLN A 168 809 253 546 -34 -286 33 C ANISOU 3 C GLN A 168 734 213 432 8 -182 -39 C ANISOU 4 O GLN A 168 837 239 506 6 -176 -49 O ANISOU 5 CB GLN A 168 887 306 708 12 -390 24 C ANISOU 6 CG GLN A 168 936 558 868 124 -449 100 C ANISOU 7 CD GLN A 168 806 281 822 12 -281 48 C ANISOU 8 OE1 GLN A 168 792 338 734 -130 -405 121 O ANISOU 9 NE2 GLN A 168 1051 360 1306 29 -219 15 N ANISOU 20 N TYR A 169 719 210 315 -63 -154 -6 N ANISOU 21 CA TYR A 169 685 127 273 -34 -202 3 C ANISOU 22 C TYR A 169 607 187 237 -54 -232 40 C ANISOU 23 O TYR A 169 586 170 232 71 -216 -7 O ANISOU 24 CB TYR A 169 758 155 310 60 -227 -28 C ANISOU 25 CG TYR A 169 850 416 337 16 -241 25 C ANISOU 26 CD1 TYR A 169 795 899 344 31 -248 68 C ANISOU 27 CD2 TYR A 169 919 585 366 -87 -229 123 C ANISOU 28 CE1 TYR A 169 883 1056 410 35 -294 -8 C ANISOU 29 CE2 TYR A 169 960 917 380 -85 -208 174 C ANISOU 30 CZ TYR A 169 922 1083 392 140 -236 33 C ANISOU 31 OH TYR A 169 997 1484 432 154 -159 56 O ANISOU 41 N SER A 170 575 175 238 28 -231 -11 N ANISOU 42 CA SER A 170 566 175 253 -29 -232 18 C ANISOU 43 C SER A 170 585 111 293 -11 -219 7 C ANISOU 44 O SER A 170 560 151 311 -21 -256 51 O ANISOU 45 CB SER A 170 763 676 530 -263 -229 -105 C ANISOU 46 OG SER A 170 828 1257 585 -265 -308 20 O ANISOU 52 N ASN A 171 600 162 297 34 -261 19 N ANISOU 53 CA ASN A 171 568 163 303 -31 -246 -5 C ANISOU 54 C ASN A 171 621 195 292 -37 -261 27 C ANISOU 55 O ASN A 171 604 186 298 -26 -250 8 O ANISOU 56 CB ASN A 171 648 198 364 -24 -305 46 C ANISOU 57 CG ASN A 171 735 236 501 -7 -382 38 C ANISOU 58 OD1 ASN A 171 713 255 508 25 -393 -32 O ANISOU 59 ND2 ASN A 171 847 284 722 -88 -274 12 N ANISOU 66 N GLN A 172 545 164 253 4 -218 3 N ANISOU 67 CA GLN A 172 543 152 262 13 -218 13 C ANISOU 68 C GLN A 172 569 173 252 -15 -230 4 C ANISOU 69 O GLN A 172 508 138 281 -78 -204 43 O ANISOU 70 CB GLN A 172 632 155 338 23 -264 15 C ANISOU 71 CG GLN A 172 772 240 451 -74 -352 81 C ANISOU 72 CD GLN A 172 722 226 510 6 -264 -14 C ANISOU 73 OE1 GLN A 172 786 233 742 -56 -137 -6 O ANISOU 74 NE2 GLN A 172 748 247 492 -67 -299 36 N ANISOU 83 N ASN A 173 614 144 273 51 -216 0 N ANISOU 84 CA ASN A 173 624 141 297 7 -224 4 C ANISOU 85 C ASN A 173 640 200 310 -46 -271 14 C ANISOU 86 O ASN A 173 605 195 331 -1 -281 4 O ANISOU 87 CB ASN A 173 673 146 287 30 -222 7 C ANISOU 88 CG ASN A 173 674 140 308 -9 -231 6 C ANISOU 89 OD1 ASN A 173 954 275 418 -48 -287 16 O ANISOU 90 ND2 ASN A 173 784 189 398 56 -305 -6 N ANISOU 97 N SER A 174 703 228 356 -61 -317 61 N ANISOU 98 CA SER A 174 717 204 453 7 -349 33 C ANISOU 99 C SER A 174 670 175 519 4 -351 -21 C ANISOU 100 O SER A 174 764 286 699 -22 -476 -18 O ANISOU 101 CB SER A 174 966 488 656 -10 -416 74 C ANISOU 102 OG SER A 174 1011 1448 810 242 -309 52 O ANISOU 108 N PHE A 175 707 253 621 -40 -307 54 N ANISOU 109 CA PHE A 175 530 194 551 -60 -183 44 C ANISOU 110 C PHE A 175 600 165 486 -71 -324 34 C ANISOU 111 O PHE A 175 705 297 543 -37 -357 50 O ANISOU 112 CB PHE A 175 481 528 704 -224 -16 232 C ANISOU 113 CG PHE A 175 395 565 709 -209 115 134 C ANISOU 114 CD1 PHE A 175 414 715 932 30 214 341 C ANISOU 115 CD2 PHE A 175 495 845 838 -284 143 168 C ANISOU 116 CE1 PHE A 175 427 1081 969 -24 263 178 C ANISOU 117 CE2 PHE A 175 589 764 955 -327 210 133 C ANISOU 118 CZ PHE A 175 391 707 809 -175 209 91 C ANISOU 128 N VAL A 176 816 378 678 65 -380 57 N ANISOU 129 CA VAL A 176 893 1087 752 31 -485 -51 C ANISOU 130 C VAL A 176 988 1360 867 224 -422 -85 C ANISOU 131 O VAL A 176 1043 1487 1007 462 -294 128 O ANISOU 132 CB VAL A 176 927 1404 840 8 -502 128 C ANISOU 133 CG1 VAL A 176 988 1749 867 -120 -424 308 C ANISOU 134 CG2 VAL A 176 942 1503 967 -56 -572 -93 C ANISOU 135 OXT VAL A 176 1025 2045 950 307 -399 -275 O TER 145 VAL A 176 HETATM 146 O HOH A 201 4.489 1.550 12.722 1.00 5.99 O ANISOU 146 O HOH A 201 599 1020 657 -47 352 92 O HETATM 147 O HOH A 202 -5.576 2.314 3.320 1.00 7.26 O ANISOU 147 O HOH A 202 556 1476 725 -25 -186 -313 O HETATM 148 O HOH A 203 15.498 3.798 22.417 1.00 17.36 O ANISOU 148 O HOH A 203 1567 3079 1951 270 196 -1205 O HETATM 149 O HOH A 204 13.735 6.537 21.899 1.00 15.21 O ANISOU 149 O HOH A 204 1862 1942 1974 -216 -82 155 O MASTER 152 0 0 0 0 0 0 6 81 1 0 1 END