HEADER TRANSCRIPTION 02-DEC-20 7B4D TITLE STRUCTURAL BASIS OF REACTIVATION OF ONCOGENIC P53 MUTANTS BY A SMALL TITLE 2 MOLECULE: METHYLENE QUINUCLIDINONE (MQ). HUMAN P53DBD-R273C/S240R TITLE 3 DOUBLE MUTANT BOUND TO DNA AND MQ: R273C/S240R-DNA-MQ 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: C; 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,Y.DISKIN-POSNER,O.DEGTJARIK,Z.SHAKKED REVDAT 3 31-JAN-24 7B4D 1 REMARK REVDAT 2 15-DEC-21 7B4D 1 JRNL REVDAT 1 08-DEC-21 7B4D 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. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 19144 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1922 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 18.2800 - 4.4400 0.99 1318 151 0.1531 0.1710 REMARK 3 2 4.4400 - 3.5300 0.99 1290 146 0.1410 0.1674 REMARK 3 3 3.5300 - 3.0900 0.98 1263 136 0.1633 0.2015 REMARK 3 4 3.0900 - 2.8100 0.98 1254 140 0.1833 0.2331 REMARK 3 5 2.8100 - 2.6100 0.97 1257 142 0.1867 0.2291 REMARK 3 6 2.6100 - 2.4500 0.96 1240 131 0.1911 0.2113 REMARK 3 7 2.4500 - 2.3300 0.96 1222 136 0.1800 0.2331 REMARK 3 8 2.3300 - 2.2300 0.95 1235 137 0.1750 0.2063 REMARK 3 9 2.2300 - 2.1400 0.95 1213 130 0.1768 0.2233 REMARK 3 10 2.1400 - 2.0700 0.95 1225 144 0.1867 0.2500 REMARK 3 11 2.0700 - 2.0100 0.94 1180 124 0.1847 0.2408 REMARK 3 12 2.0100 - 1.9500 0.94 1222 139 0.1949 0.2800 REMARK 3 13 1.9500 - 1.9000 0.93 1158 140 0.1966 0.2428 REMARK 3 14 1.9000 - 1.8500 0.89 1145 126 0.2241 0.2812 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) : 0.191 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.937 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.78 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 : 0.007 1982 REMARK 3 ANGLE : 1.239 2756 REMARK 3 CHIRALITY : 0.190 301 REMARK 3 PLANARITY : 0.006 331 REMARK 3 DIHEDRAL : 22.047 769 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 94 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): 168.4026 -12.5480 54.2568 REMARK 3 T TENSOR REMARK 3 T11: 0.2746 T22: 0.0855 REMARK 3 T33: 0.4073 T12: -0.0112 REMARK 3 T13: -0.1063 T23: 0.0299 REMARK 3 L TENSOR REMARK 3 L11: 0.8820 L22: 0.2639 REMARK 3 L33: 2.3957 L12: -0.6273 REMARK 3 L13: 0.9821 L23: -0.5074 REMARK 3 S TENSOR REMARK 3 S11: -0.4819 S12: -0.1728 S13: 0.6261 REMARK 3 S21: 0.5214 S22: 0.2112 S23: -0.5745 REMARK 3 S31: -0.5191 S32: -0.6696 S33: -0.2566 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 113 THROUGH 131 ) REMARK 3 ORIGIN FOR THE GROUP (A): 156.0249 1.1183 41.7783 REMARK 3 T TENSOR REMARK 3 T11: 0.3636 T22: 0.2509 REMARK 3 T33: 0.4161 T12: 0.0169 REMARK 3 T13: -0.0899 T23: 0.0465 REMARK 3 L TENSOR REMARK 3 L11: 1.1667 L22: 0.4008 REMARK 3 L33: 1.1100 L12: 0.6617 REMARK 3 L13: 0.7244 L23: 0.4435 REMARK 3 S TENSOR REMARK 3 S11: -0.2121 S12: 0.0269 S13: 0.7731 REMARK 3 S21: -0.6489 S22: -0.2098 S23: 0.1259 REMARK 3 S31: -0.0172 S32: -0.5123 S33: -0.1117 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 132 THROUGH 176 ) REMARK 3 ORIGIN FOR THE GROUP (A): 157.8759 -12.7415 48.9979 REMARK 3 T TENSOR REMARK 3 T11: 0.1650 T22: 0.1558 REMARK 3 T33: 0.1922 T12: 0.0223 REMARK 3 T13: -0.0122 T23: 0.0112 REMARK 3 L TENSOR REMARK 3 L11: 2.2915 L22: 1.1900 REMARK 3 L33: 0.9358 L12: -0.8558 REMARK 3 L13: 0.2461 L23: 0.0927 REMARK 3 S TENSOR REMARK 3 S11: -0.2119 S12: -0.0356 S13: 0.0883 REMARK 3 S21: 0.1044 S22: 0.0082 S23: -0.2197 REMARK 3 S31: -0.0529 S32: -0.0739 S33: -0.2316 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 177 THROUGH 194 ) REMARK 3 ORIGIN FOR THE GROUP (A): 142.8805 -21.0161 45.7291 REMARK 3 T TENSOR REMARK 3 T11: 0.2457 T22: 0.3601 REMARK 3 T33: 0.3823 T12: -0.0721 REMARK 3 T13: 0.0363 T23: -0.0943 REMARK 3 L TENSOR REMARK 3 L11: 0.6591 L22: 0.1783 REMARK 3 L33: 0.3933 L12: -0.0868 REMARK 3 L13: -0.1161 L23: -0.1136 REMARK 3 S TENSOR REMARK 3 S11: -0.2815 S12: 0.0447 S13: -1.0468 REMARK 3 S21: -0.2486 S22: -0.0981 S23: 0.4218 REMARK 3 S31: 0.4563 S32: -0.4053 S33: -0.0154 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 195 THROUGH 203 ) REMARK 3 ORIGIN FOR THE GROUP (A): 156.8154 -21.9682 38.4143 REMARK 3 T TENSOR REMARK 3 T11: 0.2869 T22: 0.2648 REMARK 3 T33: 0.1594 T12: 0.0757 REMARK 3 T13: 0.0141 T23: -0.0468 REMARK 3 L TENSOR REMARK 3 L11: 0.0054 L22: 0.1439 REMARK 3 L33: 0.0509 L12: 0.0336 REMARK 3 L13: 0.0303 L23: 0.1232 REMARK 3 S TENSOR REMARK 3 S11: 0.1738 S12: 0.6338 S13: -0.1058 REMARK 3 S21: -0.2477 S22: -0.4555 S23: 0.3015 REMARK 3 S31: 0.1467 S32: -0.3698 S33: -0.0237 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 204 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): 155.5628 -26.2223 53.4888 REMARK 3 T TENSOR REMARK 3 T11: 0.3369 T22: 0.2195 REMARK 3 T33: 0.2337 T12: 0.0226 REMARK 3 T13: 0.0629 T23: 0.0576 REMARK 3 L TENSOR REMARK 3 L11: 0.3820 L22: 0.0801 REMARK 3 L33: 0.1704 L12: 0.2292 REMARK 3 L13: -0.0970 L23: -0.0483 REMARK 3 S TENSOR REMARK 3 S11: -0.1090 S12: -0.0493 S13: -0.2801 REMARK 3 S21: 0.0764 S22: 0.2109 S23: 0.1326 REMARK 3 S31: 0.5494 S32: 0.3337 S33: 0.0841 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 214 THROUGH 229 ) REMARK 3 ORIGIN FOR THE GROUP (A): 166.8032 -16.1611 39.0159 REMARK 3 T TENSOR REMARK 3 T11: 0.2685 T22: 0.3605 REMARK 3 T33: 0.2901 T12: 0.0171 REMARK 3 T13: 0.1355 T23: 0.1454 REMARK 3 L TENSOR REMARK 3 L11: 0.5406 L22: 0.6490 REMARK 3 L33: 0.6456 L12: -0.0897 REMARK 3 L13: 0.5634 L23: 0.2603 REMARK 3 S TENSOR REMARK 3 S11: 0.2652 S12: 1.3160 S13: 0.7840 REMARK 3 S21: -0.2612 S22: 0.3496 S23: 0.0467 REMARK 3 S31: -0.2749 S32: -0.3298 S33: 0.5855 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 230 THROUGH 277 ) REMARK 3 ORIGIN FOR THE GROUP (A): 155.5225 -11.8650 49.1084 REMARK 3 T TENSOR REMARK 3 T11: 0.1617 T22: 0.1672 REMARK 3 T33: 0.1720 T12: 0.0251 REMARK 3 T13: 0.0011 T23: 0.0109 REMARK 3 L TENSOR REMARK 3 L11: 1.1536 L22: 1.0361 REMARK 3 L33: 1.5004 L12: 0.0035 REMARK 3 L13: 1.0160 L23: -0.3451 REMARK 3 S TENSOR REMARK 3 S11: -0.1725 S12: -0.1234 S13: 0.1982 REMARK 3 S21: 0.0622 S22: 0.0684 S23: -0.1689 REMARK 3 S31: -0.0455 S32: -0.1398 S33: -0.0592 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 278 THROUGH 293 ) REMARK 3 ORIGIN FOR THE GROUP (A): 151.3458 8.1235 50.6015 REMARK 3 T TENSOR REMARK 3 T11: 0.3665 T22: 0.2459 REMARK 3 T33: 0.4725 T12: 0.0662 REMARK 3 T13: -0.0930 T23: 0.0201 REMARK 3 L TENSOR REMARK 3 L11: 0.9960 L22: 0.0838 REMARK 3 L33: 1.0602 L12: 0.2675 REMARK 3 L13: -0.9415 L23: -0.1006 REMARK 3 S TENSOR REMARK 3 S11: 0.2125 S12: -0.2137 S13: 0.2603 REMARK 3 S21: -0.0760 S22: -0.2477 S23: 0.0873 REMARK 3 S31: -0.0300 S32: 0.4211 S33: 0.0329 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 134.3477 4.6031 53.3153 REMARK 3 T TENSOR REMARK 3 T11: 0.4827 T22: 0.6209 REMARK 3 T33: 0.2597 T12: 0.0173 REMARK 3 T13: -0.0515 T23: 0.0626 REMARK 3 L TENSOR REMARK 3 L11: 0.1909 L22: 0.3249 REMARK 3 L33: 0.2858 L12: 0.0041 REMARK 3 L13: -0.3085 L23: -0.1898 REMARK 3 S TENSOR REMARK 3 S11: -0.0585 S12: -0.1639 S13: -0.0361 REMARK 3 S21: 0.1136 S22: 0.1484 S23: -0.1061 REMARK 3 S31: -0.0686 S32: -0.1180 S33: 0.1072 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 7B4D 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_1292111699. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.1 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 : MIRRORS 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 : 19150 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.50800 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 (%): 45.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN/DNA RATIO 1:2.4, 0.2M SODIUM REMARK 280 FORMATE, 20% W/V PEG 3350, PH 6.1, 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 68.79350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.08200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.79350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.08200 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: 4840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 270.51912 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 102.58745 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 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 LEU A 188 CG CD1 CD2 REMARK 470 ARG A 248 CD NE CZ NH1 NH2 REMARK 470 GLU A 287 CG CD OE1 OE2 REMARK 470 ARG A 290 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 291 CD CE NZ REMARK 470 DC C 11 C2 O2 N3 C4 N4 C5 C6 REMARK 470 DG C 12 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DG C 12 N9 C8 N7 C5 C6 O6 N1 REMARK 470 DG C 12 C2 N2 N3 C4 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 DC C 9 O4' - C1' - N1 ANGL. DEV. = 1.8 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 540 DISTANCE = 6.62 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 TWO ENANTIOMERS, QNN AND QN8 ARE PRODUCED BY ADDITION REACTION OF REMARK 600 THE MICHAEL ACCEPTOR COMPOUND "2-METHYLENEQUINUCLIDIN-3-ONE" WITH REMARK 600 CYSTEINE OR LYSINE. AS SUCH, QNN AND QN8 BIND COVALENTLY TO THE REMARK 600 THIOL GROUP OF CYSTEINE OR AMINO GROUP OF LYSINE. THE CHIRAL REMARK 600 DEFINITIONS OF QNN AND QN8 BOUND TO CYSTEINES ARE REVERSED TO THAT REMARK 600 OF THE PSEUDO FREE LIGANDS. 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 103.4 REMARK 620 3 CYS A 238 SG 109.2 112.6 REMARK 620 4 CYS A 242 SG 112.5 102.0 116.2 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: 7B4E RELATED DB: PDB REMARK 900 PROTEIN-DNA COMPLEX REMARK 900 RELATED ID: 7B4F 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 7B4D A 94 293 UNP P04637 P53_HUMAN 94 293 DBREF 7B4D C 1 12 PDB 7B4D 7B4D 1 12 SEQADV 7B4D ARG A 240 UNP P04637 SER 240 ENGINEERED MUTATION SEQADV 7B4D CYS A 273 UNP P04637 ARG 273 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 ARG 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 CYS VAL CYS SEQRES 15 A 200 ALA CYS PRO GLY ARG ASP ARG ARG THR GLU GLU GLU ASN SEQRES 16 A 200 LEU ARG LYS LYS GLY SEQRES 1 C 12 DC DG DG DG DC DA DT DG DC DC DC DG HET ZN A 301 1 HET QNN A 302 10 HET QN8 A 303 10 HET QNN A 304 10 HET QNN A 305 10 HET FMT A 306 3 HET FMT A 307 3 HET FMT A 308 3 HETNAM ZN ZINC ION HETNAM QNN (2~{S})-2-METHYL-1-AZABICYCLO[2.2.2]OCTAN-3-ONE HETNAM QN8 (2~{R})-2-METHYL-1-AZABICYCLO[2.2.2]OCTAN-3-ONE HETNAM FMT FORMIC ACID FORMUL 3 ZN ZN 2+ FORMUL 4 QNN 3(C8 H13 N O) FORMUL 5 QN8 C8 H13 N O FORMUL 8 FMT 3(C H2 O2) FORMUL 11 HOH *148(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 THR A 140 TRP A 146 -1 O GLN A 144 N GLY A 112 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 LYS A 132 N SER A 127 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 MET A 160 O ILE A 254 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 BCYS A 124 C1 BQNN A 302 1555 1555 1.80 LINK SG BCYS A 229 C1 BQN8 A 303 1555 1555 1.85 LINK SG CCYS A 229 C1 CQNN A 304 1555 1555 1.80 LINK SG BCYS A 277 C1 BQNN A 305 1555 1555 1.73 LINK SG CYS A 176 ZN ZN A 301 1555 1555 2.31 LINK ND1 HIS A 179 ZN ZN A 301 1555 1555 2.02 LINK SG CYS A 238 ZN ZN A 301 1555 1555 2.32 LINK SG CYS A 242 ZN ZN A 301 1555 1555 2.34 CRYST1 137.587 50.164 34.231 90.00 92.60 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 0.007268 0.000000 0.000330 0.00000 SCALE2 0.000000 0.019935 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029243 0.00000