HEADER ANTITUMOR PROTEIN 30-SEP-13 4MZI TITLE CRYSTAL STRUCTURE OF A HUMAN MUTANT P53 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULAR TUMOR ANTIGEN P53; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 94-292; COMPND 5 SYNONYM: ANTIGEN NY-CO-13, PHOSPHOPROTEIN P53, TUMOR SUPPRESSOR P53; COMPND 6 ENGINEERED: YES; COMPND 7 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LOOP L1, TUMOR SUPPRESSOR, ANTITUMOUR PROTEIN, DNA BINDING, ANTITUMOR KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.EMAMZADAH,L.TROPIA,I.VINCENTI,B.FALQUET,T.D.HALAZONETIS REVDAT 4 21-DEC-22 4MZI 1 REMARK SEQADV REVDAT 3 09-APR-14 4MZI 1 SEQADV REVDAT 2 12-FEB-14 4MZI 1 JRNL REVDAT 1 15-JAN-14 4MZI 0 JRNL AUTH S.EMAMZADAH,L.TROPIA,I.VINCENTI,B.FALQUET,T.D.HALAZONETIS JRNL TITL REVERSAL OF THE DNA-BINDING-INDUCED LOOP L1 CONFORMATIONAL JRNL TITL 2 SWITCH IN AN ENGINEERED HUMAN P53 PROTEIN. JRNL REF J.MOL.BIOL. V. 426 936 2014 JRNL REFN ISSN 0022-2836 JRNL PMID 24374182 JRNL DOI 10.1016/J.JMB.2013.12.020 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 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 : 8315 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 57048 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 : 1518 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 214 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL 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 4MZI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000082561. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 85 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93340 REMARK 200 MONOCHROMATOR : PT COATED SI MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8315 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.8, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 22.35350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.85050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.21400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.85050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.35350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.21400 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A 93 REMARK 465 SER A 94 REMARK 465 SER A 95 REMARK 465 LEU A 289 REMARK 465 ARG A 290 REMARK 465 LYS A 291 REMARK 465 LYS A 292 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 188 -83.51 -71.80 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 A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 176 SG REMARK 620 2 CYS A 238 SG 111.6 REMARK 620 3 CYS A 242 SG 112.3 114.9 REMARK 620 N 1 2 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 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4MZR RELATED DB: PDB DBREF 4MZI A 94 292 UNP P04637 P53_HUMAN 94 292 SEQADV 4MZI MET A 93 UNP P04637 INITIATING METHIONINE SEQADV 4MZI PHE A 121 UNP P04637 SER 121 ENGINEERED MUTATION SEQADV 4MZI GLY A 122 UNP P04637 VAL 122 ENGINEERED MUTATION SEQADV 4MZI VAL A 135 UNP P04637 CYS 135 CONFLICT SEQADV 4MZI VAL A 141 UNP P04637 CYS 141 CONFLICT SEQADV 4MZI TYR A 146 UNP P04637 TRP 146 CONFLICT SEQADV 4MZI SER A 182 UNP P04637 CYS 182 VARIANT SEQADV 4MZI ALA A 203 UNP P04637 VAL 203 VARIANT SEQADV 4MZI PRO A 209 UNP P04637 ARG 209 CONFLICT SEQADV 4MZI TYR A 229 UNP P04637 CYS 229 VARIANT SEQADV 4MZI TYR A 233 UNP P04637 HIS 233 VARIANT SEQADV 4MZI PHE A 234 UNP P04637 TYR 234 VARIANT SEQADV 4MZI LYS A 235 UNP P04637 ASN 235 CONFLICT SEQADV 4MZI PHE A 236 UNP P04637 TYR 236 VARIANT SEQADV 4MZI VAL A 253 UNP P04637 THR 253 CONFLICT SEQADV 4MZI ASP A 268 UNP P04637 ASN 268 CONFLICT SEQRES 1 A 200 MET SER SER SER VAL PRO SER GLN LYS THR TYR GLN GLY SEQRES 2 A 200 SER TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY THR SEQRES 3 A 200 ALA LYS PHE GLY THR CYS THR TYR SER PRO ALA LEU ASN SEQRES 4 A 200 LYS MET PHE VAL GLN LEU ALA LYS THR VAL PRO VAL GLN SEQRES 5 A 200 LEU TYR VAL ASP SER THR PRO PRO PRO GLY THR ARG VAL SEQRES 6 A 200 ARG ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET THR SEQRES 7 A 200 GLU VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG SER SER SEQRES 8 A 200 ASP SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE ARG SEQRES 9 A 200 VAL GLU GLY ASN LEU ARG ALA GLU TYR LEU ASP ASP PRO SEQRES 10 A 200 ASN THR PHE ARG HIS SER VAL VAL VAL PRO TYR GLU PRO SEQRES 11 A 200 PRO GLU VAL GLY SER ASP TYR THR THR ILE TYR PHE LYS SEQRES 12 A 200 PHE MET CYS ASN SER SER CYS MET GLY GLY MET ASN ARG SEQRES 13 A 200 ARG PRO ILE LEU VAL ILE ILE THR LEU GLU ASP SER SER SEQRES 14 A 200 GLY ASN LEU LEU GLY ARG ASP SER PHE GLU VAL ARG VAL SEQRES 15 A 200 CYS ALA CYS PRO GLY ARG ASP ARG ARG THR GLU GLU GLU SEQRES 16 A 200 ASN LEU ARG LYS LYS HET ZN A 301 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *214(H2 O) HELIX 1 1 GLN A 165 MET A 169 5 5 HELIX 2 2 CYS A 176 ARG A 181 1 6 HELIX 3 3 CYS A 277 ASN A 288 1 12 SHEET 1 A 4 ARG A 110 GLY A 112 0 SHEET 2 A 4 VAL A 141 TYR A 146 -1 O GLN A 144 N GLY A 112 SHEET 3 A 4 THR A 230 PHE A 236 -1 O THR A 230 N LEU A 145 SHEET 4 A 4 ILE A 195 GLU A 198 -1 N GLU A 198 O TYR A 233 SHEET 1 B 7 CYS A 124 SER A 127 0 SHEET 2 B 7 LYS A 132 VAL A 135 -1 O LYS A 132 N SER A 127 SHEET 3 B 7 LEU A 264 VAL A 274 1 O GLU A 271 N MET A 133 SHEET 4 B 7 ILE A 251 GLU A 258 -1 N VAL A 253 O PHE A 270 SHEET 5 B 7 ARG A 156 TYR A 163 -1 N MET A 160 O ILE A 254 SHEET 6 B 7 HIS A 214 PRO A 219 -1 O VAL A 218 N VAL A 157 SHEET 7 B 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 2.34 LINK SG CYS A 238 ZN ZN A 301 1555 1555 2.37 LINK SG CYS A 242 ZN ZN A 301 1555 1555 2.37 SITE 1 AC1 4 CYS A 176 HIS A 179 CYS A 238 CYS A 242 CRYST1 44.707 62.428 73.701 90.00 90.00 90.00 P 21 21 21 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 0.022368 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016018 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013568 0.00000