HEADER TRANSCRIPTION 02-DEC-20 7B4F TITLE STRUCTURAL BASIS OF REACTIVATION OF ONCOGENIC P53 MUTANTS BY A SMALL TITLE 2 MOLECULE: METHYLENE QUINUCLIDINONE (MQ). HUMAN P53DBD-R282W MUTANT TITLE 3 BOUND TO DNA: R282W-MQ (I) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULAR TUMOR ANTIGEN P53; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: P53 HUMAN DNA BINDING DOMAIN; COMPND 5 SYNONYM: ANTIGEN NY-CO-13,PHOSPHOPROTEIN P53,TUMOR SUPPRESSOR P53; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA TARGET; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: P53 DNA TARGET; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TP53, P53; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-27-B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 OTHER_DETAILS: IDT: INTEGRATED DNA TECHNOLOGY KEYWDS P53, TUMOR SUPPRESSOR, DNA BINDING PROTEIN, PROTEIN DNA COMPLEX, KEYWDS 2 MICHAEL ACCEPTOR, MICHAEL REACTION, PROTEIN-DRUG COMPLEX, PROTEIN- KEYWDS 3 DNA-DRUG COMPLEX, LOOP-SHEET-HELIX MOTIF, DNA TARGET, ACTIVATOR, KEYWDS 4 TRANSCRIPTION, HOOGSTEEN BASE-PAIRING EXPDTA X-RAY DIFFRACTION AUTHOR H.ROZENBERG,O.DEGTJARIK,Z.SHAKKED REVDAT 3 31-JAN-24 7B4F 1 REMARK REVDAT 2 15-DEC-21 7B4F 1 JRNL REVDAT 1 08-DEC-21 7B4F 0 JRNL AUTH O.DEGTJARIK,D.GOLOVENKO,Y.DISKIN-POSNER,L.ABRAHMSEN, JRNL AUTH 2 H.ROZENBERG,Z.SHAKKED JRNL TITL STRUCTURAL BASIS OF REACTIVATION OF ONCOGENIC P53 MUTANTS BY JRNL TITL 2 A SMALL MOLECULE: METHYLENE QUINUCLIDINONE (MQ). JRNL REF NAT COMMUN V. 12 7057 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34862374 JRNL DOI 10.1038/S41467-021-27142-6 REMARK 2 REMARK 2 RESOLUTION. 1.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2-3874 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) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 21071 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2108 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 18.4200 - 4.3700 1.00 1365 152 0.1371 0.1626 REMARK 3 2 4.3600 - 3.4700 0.99 1326 142 0.1295 0.1761 REMARK 3 3 3.4700 - 3.0400 0.98 1290 152 0.1453 0.1699 REMARK 3 4 3.0400 - 2.7600 0.97 1284 141 0.1695 0.1915 REMARK 3 5 2.7600 - 2.5600 0.97 1296 149 0.1680 0.2367 REMARK 3 6 2.5600 - 2.4100 0.98 1288 132 0.1707 0.2248 REMARK 3 7 2.4100 - 2.2900 0.95 1264 146 0.1608 0.2070 REMARK 3 8 2.2900 - 2.1900 0.95 1268 143 0.1519 0.1833 REMARK 3 9 2.1900 - 2.1100 0.97 1249 144 0.1599 0.1987 REMARK 3 10 2.1100 - 2.0300 0.93 1237 138 0.1618 0.2123 REMARK 3 11 2.0300 - 1.9700 0.96 1246 134 0.1681 0.2363 REMARK 3 12 1.9700 - 1.9100 0.93 1232 131 0.1796 0.2068 REMARK 3 13 1.9100 - 1.8600 0.94 1222 139 0.1839 0.2383 REMARK 3 14 1.8600 - 1.8200 0.93 1213 148 0.1864 0.2480 REMARK 3 15 1.8200 - 1.7800 0.90 1183 117 0.2271 0.2530 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) : 0.169 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.56 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 : 0.005 1917 REMARK 3 ANGLE : 0.723 2661 REMARK 3 CHIRALITY : 0.051 289 REMARK 3 PLANARITY : 0.005 322 REMARK 3 DIHEDRAL : 22.228 744 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 94 THROUGH 123 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.8616 -9.6211 14.8964 REMARK 3 T TENSOR REMARK 3 T11: 0.1532 T22: 0.1938 REMARK 3 T33: 0.2481 T12: -0.0051 REMARK 3 T13: -0.0061 T23: 0.0465 REMARK 3 L TENSOR REMARK 3 L11: 0.3605 L22: 0.5989 REMARK 3 L33: 0.1624 L12: -0.2929 REMARK 3 L13: -0.0853 L23: 0.3289 REMARK 3 S TENSOR REMARK 3 S11: -0.0911 S12: -0.0373 S13: 0.1789 REMARK 3 S21: 0.1551 S22: 0.0239 S23: -0.2621 REMARK 3 S31: -0.0544 S32: -0.0665 S33: -0.0084 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 124 THROUGH 140 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.8182 -4.3402 9.7179 REMARK 3 T TENSOR REMARK 3 T11: 0.1650 T22: 0.2136 REMARK 3 T33: 0.1758 T12: -0.0131 REMARK 3 T13: -0.0191 T23: 0.0050 REMARK 3 L TENSOR REMARK 3 L11: 0.1130 L22: 0.1479 REMARK 3 L33: 0.0760 L12: -0.0819 REMARK 3 L13: -0.0330 L23: 0.1127 REMARK 3 S TENSOR REMARK 3 S11: -0.0167 S12: 0.2749 S13: 0.2295 REMARK 3 S21: 0.0491 S22: 0.0151 S23: -0.1104 REMARK 3 S31: 0.0337 S32: 0.1567 S33: -0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 141 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.9410 -14.8296 7.3383 REMARK 3 T TENSOR REMARK 3 T11: 0.1409 T22: 0.1914 REMARK 3 T33: 0.2974 T12: -0.0113 REMARK 3 T13: -0.0047 T23: 0.0837 REMARK 3 L TENSOR REMARK 3 L11: 0.1444 L22: 0.0964 REMARK 3 L33: 0.2111 L12: 0.0577 REMARK 3 L13: -0.0653 L23: 0.0907 REMARK 3 S TENSOR REMARK 3 S11: -0.0691 S12: 0.4463 S13: 0.0983 REMARK 3 S21: -0.1986 S22: 0.0313 S23: -0.1550 REMARK 3 S31: -0.0109 S32: -0.0597 S33: 0.0615 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 203 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.2816 -19.0337 15.6380 REMARK 3 T TENSOR REMARK 3 T11: 0.1596 T22: 0.1453 REMARK 3 T33: 0.1303 T12: -0.0045 REMARK 3 T13: 0.0025 T23: -0.0067 REMARK 3 L TENSOR REMARK 3 L11: 0.6883 L22: 0.5549 REMARK 3 L33: 0.3259 L12: -0.5797 REMARK 3 L13: 0.1175 L23: -0.2506 REMARK 3 S TENSOR REMARK 3 S11: -0.0580 S12: 0.0324 S13: -0.0834 REMARK 3 S21: 0.0435 S22: -0.0418 S23: 0.0637 REMARK 3 S31: 0.0611 S32: -0.0479 S33: -0.0026 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 204 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.8498 -27.4877 19.4247 REMARK 3 T TENSOR REMARK 3 T11: 0.2754 T22: 0.1907 REMARK 3 T33: 0.1677 T12: 0.0093 REMARK 3 T13: 0.0247 T23: 0.0119 REMARK 3 L TENSOR REMARK 3 L11: 0.8000 L22: 0.1037 REMARK 3 L33: 0.0369 L12: -0.2025 REMARK 3 L13: 0.1613 L23: -0.0251 REMARK 3 S TENSOR REMARK 3 S11: 0.1524 S12: 0.0032 S13: -0.3223 REMARK 3 S21: 0.1366 S22: 0.0859 S23: 0.1881 REMARK 3 S31: 0.1219 S32: 0.1704 S33: 0.0741 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 214 THROUGH 229 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.2507 -18.2920 4.5671 REMARK 3 T TENSOR REMARK 3 T11: 0.2125 T22: 0.3578 REMARK 3 T33: 0.2429 T12: 0.0173 REMARK 3 T13: 0.0835 T23: 0.1246 REMARK 3 L TENSOR REMARK 3 L11: 0.0088 L22: 0.1865 REMARK 3 L33: 0.3630 L12: -0.0102 REMARK 3 L13: 0.0230 L23: -0.1464 REMARK 3 S TENSOR REMARK 3 S11: 0.0149 S12: 0.6589 S13: 0.3723 REMARK 3 S21: -0.2357 S22: 0.0712 S23: -0.0869 REMARK 3 S31: 0.0281 S32: -0.0033 S33: -0.0389 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 230 THROUGH 277 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.0507 -13.2198 14.7281 REMARK 3 T TENSOR REMARK 3 T11: 0.1536 T22: 0.1474 REMARK 3 T33: 0.1487 T12: 0.0038 REMARK 3 T13: -0.0010 T23: 0.0061 REMARK 3 L TENSOR REMARK 3 L11: 0.2830 L22: 0.7376 REMARK 3 L33: 0.3349 L12: -0.1332 REMARK 3 L13: 0.1602 L23: -0.0462 REMARK 3 S TENSOR REMARK 3 S11: -0.0308 S12: 0.0800 S13: 0.0586 REMARK 3 S21: 0.0507 S22: -0.0257 S23: -0.0962 REMARK 3 S31: -0.0163 S32: -0.0019 S33: 0.0000 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 278 THROUGH 293 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.1942 6.6095 15.1874 REMARK 3 T TENSOR REMARK 3 T11: 0.1738 T22: 0.1494 REMARK 3 T33: 0.2375 T12: 0.0112 REMARK 3 T13: -0.0055 T23: 0.0256 REMARK 3 L TENSOR REMARK 3 L11: 0.2418 L22: 0.0694 REMARK 3 L33: 0.4714 L12: -0.0502 REMARK 3 L13: -0.2825 L23: 0.1533 REMARK 3 S TENSOR REMARK 3 S11: 0.0121 S12: 0.0143 S13: 0.2348 REMARK 3 S21: -0.1493 S22: 0.0611 S23: 0.0599 REMARK 3 S31: -0.1533 S32: 0.1120 S33: 0.0698 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.5107 3.5088 13.8832 REMARK 3 T TENSOR REMARK 3 T11: 0.2145 T22: 0.2070 REMARK 3 T33: 0.1797 T12: -0.0054 REMARK 3 T13: -0.0109 T23: -0.0167 REMARK 3 L TENSOR REMARK 3 L11: 0.2027 L22: 0.1997 REMARK 3 L33: 0.2819 L12: 0.1047 REMARK 3 L13: -0.1198 L23: 0.1265 REMARK 3 S TENSOR REMARK 3 S11: 0.0418 S12: 0.0133 S13: 0.1170 REMARK 3 S21: -0.0557 S22: 0.1044 S23: 0.0612 REMARK 3 S31: -0.1573 S32: 0.0219 S33: 0.0142 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 7B4F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1292111701. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-09 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : VARIMAX OPTICS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21071 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.780 REMARK 200 RESOLUTION RANGE LOW (A) : 21.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.45200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 2AC0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN/DNA RATIO 1:1.5, 0.03M CITRIC REMARK 280 ACID, 0.07M BIS-TRIS PROPANE PH=7.6, 20% W/V PEG 3350, REMARK 280 EVAPORATION, TEMPERATURE 292K 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 68.60500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.87150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.60500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.87150 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: TETRAMER REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMER REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -1.98017 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 33.75797 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 183 REMARK 465 ASP A 184 REMARK 465 SER A 185 REMARK 465 ASP A 186 REMARK 465 DG B 12 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 HIS A 115 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 188 CG CD1 CD2 REMARK 470 GLU A 198 CD OE1 OE2 REMARK 470 GLU A 287 CG CD OE1 OE2 REMARK 470 LYS A 291 CD CE NZ REMARK 470 LYS A 292 CD CE NZ REMARK 470 DC B 11 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DC B 11 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC B 11 C6 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG B 4 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 638 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 639 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH A 640 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH B 155 DISTANCE = 6.46 ANGSTROMS 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 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 176 SG REMARK 620 2 HIS A 179 ND1 102.4 REMARK 620 3 CYS A 238 SG 109.5 112.7 REMARK 620 4 CYS A 242 SG 115.1 102.9 113.5 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6ZNC RELATED DB: PDB REMARK 900 PROTEIN/DNA COMPLEX REMARK 900 RELATED ID: 7B47 RELATED DB: PDB REMARK 900 RELATED ID: 7B49 RELATED DB: PDB REMARK 900 PROTEIN/DNA COMPLEX REMARK 900 RELATED ID: 7B4A RELATED DB: PDB REMARK 900 PROTEIN/DNA COMPLEX REMARK 900 RELATED ID: 7B4B RELATED DB: PDB REMARK 900 RELATED ID: 7B4D RELATED DB: PDB REMARK 900 PROTEIN/DNA COMPLEX REMARK 900 RELATED ID: 7B4E RELATED DB: PDB REMARK 900 PROTEIN/DNA COMPLEX REMARK 900 RELATED ID: 7B4G RELATED DB: PDB REMARK 900 PROTEIN/DNA COMPLEX REMARK 900 RELATED ID: 7B4N RELATED DB: PDB REMARK 900 PROTEIN/DNA COMPLEX REMARK 900 RELATED ID: 7B4H RELATED DB: PDB REMARK 900 PROTEIN/DNA COMPLEX REMARK 900 RELATED ID: 7B46 RELATED DB: PDB REMARK 900 PROTEIN/DNA COMPLEX REMARK 900 RELATED ID: 7B48 RELATED DB: PDB REMARK 900 RELATED ID: 7B4C RELATED DB: PDB DBREF 7B4F A 94 293 UNP P04637 P53_HUMAN 94 293 DBREF 7B4F B 1 12 PDB 7B4F 7B4F 1 12 SEQADV 7B4F TRP A 282 UNP P04637 ARG 282 ENGINEERED MUTATION SEQRES 1 A 200 SER SER SER VAL PRO SER GLN LYS THR TYR GLN GLY SER SEQRES 2 A 200 TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY THR ALA SEQRES 3 A 200 LYS SER VAL THR CYS THR TYR SER PRO ALA LEU ASN LYS SEQRES 4 A 200 MET PHE CYS GLN LEU ALA LYS THR CYS PRO VAL GLN LEU SEQRES 5 A 200 TRP VAL ASP SER THR PRO PRO PRO GLY THR ARG VAL ARG SEQRES 6 A 200 ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET THR GLU SEQRES 7 A 200 VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SER ASP SEQRES 8 A 200 SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE ARG VAL SEQRES 9 A 200 GLU GLY ASN LEU ARG VAL GLU TYR LEU ASP ASP ARG ASN SEQRES 10 A 200 THR PHE ARG HIS SER VAL VAL VAL PRO TYR GLU PRO PRO SEQRES 11 A 200 GLU VAL GLY SER ASP CYS THR THR ILE HIS TYR ASN TYR SEQRES 12 A 200 MET CYS ASN SER SER CYS MET GLY GLY MET ASN ARG ARG SEQRES 13 A 200 PRO ILE LEU THR ILE ILE THR LEU GLU ASP SER SER GLY SEQRES 14 A 200 ASN LEU LEU GLY ARG ASN SER PHE GLU VAL ARG VAL CYS SEQRES 15 A 200 ALA CYS PRO GLY ARG ASP TRP ARG THR GLU GLU GLU ASN SEQRES 16 A 200 LEU ARG LYS LYS GLY SEQRES 1 B 12 DC DG DG DG DC DA DT DG DC DC DC DG HET ZN A 301 1 HET FMT A 302 3 HET FMT A 303 3 HETNAM ZN ZINC ION HETNAM FMT FORMIC ACID FORMUL 3 ZN ZN 2+ FORMUL 4 FMT 2(C H2 O2) FORMUL 6 HOH *295(H2 O) HELIX 1 AA1 GLN A 165 MET A 169 5 5 HELIX 2 AA2 CYS A 176 CYS A 182 1 7 HELIX 3 AA3 CYS A 277 GLY A 293 1 17 SHEET 1 AA1 4 ARG A 110 GLY A 112 0 SHEET 2 AA1 4 CYS A 141 TRP A 146 -1 O TRP A 146 N ARG A 110 SHEET 3 AA1 4 THR A 230 TYR A 236 -1 O THR A 230 N LEU A 145 SHEET 4 AA1 4 ILE A 195 GLU A 198 -1 N ARG A 196 O ASN A 235 SHEET 1 AA2 7 CYS A 124 SER A 127 0 SHEET 2 AA2 7 LYS A 132 CYS A 135 -1 O PHE A 134 N THR A 125 SHEET 3 AA2 7 LEU A 264 VAL A 274 1 O GLU A 271 N MET A 133 SHEET 4 AA2 7 ILE A 251 GLU A 258 -1 N LEU A 257 O LEU A 265 SHEET 5 AA2 7 ARG A 156 TYR A 163 -1 N ARG A 156 O GLU A 258 SHEET 6 AA2 7 HIS A 214 PRO A 219 -1 O VAL A 218 N VAL A 157 SHEET 7 AA2 7 GLU A 204 ASP A 207 -1 N GLU A 204 O VAL A 217 LINK SG CYS A 176 ZN ZN A 301 1555 1555 2.33 LINK ND1 HIS A 179 ZN ZN A 301 1555 1555 2.04 LINK SG CYS A 238 ZN ZN A 301 1555 1555 2.33 LINK SG CYS A 242 ZN ZN A 301 1555 1555 2.33 CRYST1 137.210 49.743 33.816 90.00 93.36 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 0.007288 0.000000 0.000428 0.00000 SCALE2 0.000000 0.020103 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029623 0.00000