HEADER TRANSCRIPTION, ANTITUMOR PROTEIN 10-OCT-06 2IOO TITLE CRYSTAL STRUCTURE OF THE MOUSE P53 CORE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULAR TUMOR ANTIGEN P53; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MOUSE P53 CORE DOMAIN, RESIDUES 92-292; COMPND 5 SYNONYM: TUMOR SUPPRESSOR P53; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: TP53, P53, TRP53; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSETA KEYWDS IG FOLD, TRANSCRIPTION, ANTITUMOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.C.HO,C.LUO,K.ZHAO,X.CHAI,M.X.FITZGERALD,R.MARMORSTEIN REVDAT 4 21-FEB-24 2IOO 1 REMARK LINK REVDAT 3 18-OCT-17 2IOO 1 REMARK REVDAT 2 24-FEB-09 2IOO 1 VERSN REVDAT 1 05-DEC-06 2IOO 0 JRNL AUTH W.C.HO,C.LUO,K.ZHAO,X.CHAI,M.X.FITZGERALD,R.MARMORSTEIN JRNL TITL HIGH-RESOLUTION STRUCTURE OF THE P53 CORE DOMAIN: JRNL TITL 2 IMPLICATIONS FOR BINDING SMALL-MOLECULE STABILIZING JRNL TITL 3 COMPOUNDS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 62 1484 2006 JRNL REFN ISSN 0907-4449 JRNL PMID 17139084 JRNL DOI 10.1107/S090744490603890X REMARK 2 REMARK 2 RESOLUTION. 2.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 13086 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1471 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 176 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.330 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2IOO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000039825. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 92.15 REMARK 200 PH : 7.0 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13086 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.020 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.8200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 50.00 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.19800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.820 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: MOUSE P53 CORE DOMAIN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES, 16-18% PEG 2K MME, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 45.78400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.35450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.78400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.35450 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 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 1092 REMARK 465 PHE A 1093 REMARK 465 VAL A 1094 REMARK 465 PRO A 1095 REMARK 465 SER A 1096 REMARK 465 GLU A 1284 REMARK 465 ASN A 1285 REMARK 465 PHE A 1286 REMARK 465 ARG A 1287 REMARK 465 LYS A 1288 REMARK 465 LYS A 1289 REMARK 465 GLU A 1290 REMARK 465 VAL A 1291 REMARK 465 LEU A 1292 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 LYS A1117 CB CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 4109 O HOH A 4153 2555 2.08 REMARK 500 REMARK 500 REMARK: NULL 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 A3001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1173 SG REMARK 620 2 HIS A1176 ND1 102.9 REMARK 620 3 CYS A1235 SG 112.5 107.6 REMARK 620 4 CYS A1239 SG 113.1 106.1 113.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 3001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IOI RELATED DB: PDB REMARK 900 HIGH-RESOLUTION STRUCTURE OF THE P53 CORE DOMAIN: IMPLICATIONS FOR REMARK 900 BINDING SMALL-MOLECULE STABILIZING COMPOUNDS REMARK 900 RELATED ID: 2IOM RELATED DB: PDB REMARK 900 MOUSE P53 CORE DOMAIN SOAKED WITH 2-PROPANOL DBREF 2IOO A 1092 1292 UNP P02340 P53_MOUSE 92 292 SEQRES 1 A 201 SER PHE VAL PRO SER GLN LYS THR TYR GLN GLY ASN TYR SEQRES 2 A 201 GLY PHE HIS LEU GLY PHE LEU GLN SER GLY THR ALA LYS SEQRES 3 A 201 SER VAL MET CYS THR TYR SER PRO PRO LEU ASN LYS LEU SEQRES 4 A 201 PHE CYS GLN LEU ALA LYS THR CYS PRO VAL GLN LEU TRP SEQRES 5 A 201 VAL SER ALA THR PRO PRO ALA GLY SER ARG VAL ARG ALA SEQRES 6 A 201 MET ALA ILE TYR LYS LYS SER GLN HIS MET THR GLU VAL SEQRES 7 A 201 VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SER ASP GLY SEQRES 8 A 201 ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE ARG VAL GLU SEQRES 9 A 201 GLY ASN LEU TYR PRO GLU TYR LEU GLU ASP ARG GLN THR SEQRES 10 A 201 PHE ARG HIS SER VAL VAL VAL PRO TYR GLU PRO PRO GLU SEQRES 11 A 201 ALA GLY SER GLU TYR THR THR ILE HIS TYR LYS TYR MET SEQRES 12 A 201 CYS ASN SER SER CYS MET GLY GLY MET ASN ARG ARG PRO SEQRES 13 A 201 ILE LEU THR ILE ILE THR LEU GLU ASP SER SER GLY ASN SEQRES 14 A 201 LEU LEU GLY ARG ASP SER PHE GLU VAL ARG VAL CYS ALA SEQRES 15 A 201 CYS PRO GLY ARG ASP ARG ARG THR GLU GLU GLU ASN PHE SEQRES 16 A 201 ARG LYS LYS GLU VAL LEU HET ZN A3001 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *176(H2 O) HELIX 1 1 GLN A 1101 GLY A 1105 5 5 HELIX 2 2 CYS A 1173 ARG A 1178 1 6 HELIX 3 3 CYS A 1274 GLU A 1283 1 10 SHEET 1 A 4 HIS A1107 GLY A1109 0 SHEET 2 A 4 CYS A1138 TRP A1143 -1 O TRP A1143 N HIS A1107 SHEET 3 A 4 THR A1227 TYR A1233 -1 O THR A1227 N LEU A1142 SHEET 4 A 4 ILE A1192 GLU A1195 -1 N GLU A1195 O HIS A1230 SHEET 1 B 7 CYS A1121 SER A1124 0 SHEET 2 B 7 LYS A1129 CYS A1132 -1 O PHE A1131 N THR A1122 SHEET 3 B 7 LEU A1261 VAL A1271 1 O GLU A1268 N LEU A1130 SHEET 4 B 7 ILE A1248 GLU A1255 -1 N LEU A1254 O LEU A1262 SHEET 5 B 7 ARG A1153 TYR A1160 -1 N MET A1157 O ILE A1251 SHEET 6 B 7 HIS A1211 PRO A1216 -1 O VAL A1215 N VAL A1154 SHEET 7 B 7 GLU A1201 GLU A1204 -1 N LEU A1203 O SER A1212 LINK SG CYS A1173 ZN ZN A3001 1555 1555 2.35 LINK ND1 HIS A1176 ZN ZN A3001 1555 1555 1.99 LINK SG CYS A1235 ZN ZN A3001 1555 1555 2.31 LINK SG CYS A1239 ZN ZN A3001 1555 1555 2.41 SITE 1 AC1 4 CYS A1173 HIS A1176 CYS A1235 CYS A1239 CRYST1 91.568 44.709 62.607 90.00 125.61 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 0.010921 0.000000 0.007821 0.00000 SCALE2 0.000000 0.022367 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019647 0.00000