HEADER TRANSCRIPTION 24-OCT-23 8UQR TITLE CRYSTAL STRUCTURE OF THE HUMAN P53 TETRAMERIZATION DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULAR TUMOR ANTIGEN P53; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: 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; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HUMAN P53 TETRAMERIZATION DOMAIN STABILITY, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR H.M.WAHBA,S.SAKAGUCHI,N.NAKAGAWA,J.WADA,R.KAMADA,K.SAKAGUCHI, AUTHOR 2 J.G.OMICHINSKI REVDAT 1 20-DEC-23 8UQR 0 JRNL AUTH S.SAKAGUCHI,N.NAKAGAWA,H.M.WAHBA,J.WADA,R.KAMADA, JRNL AUTH 2 J.G.OMICHINSKI,K.SAKAGUCHI JRNL TITL HIGHLY SIMILAR TETRAMERIZATION DOMAINS FROM THE P53 PROTEIN JRNL TITL 2 OF DIFFERENT MAMMALIAN SPECIES POSSESS VARYING BIOPHYSICAL, JRNL TITL 3 FUNCTIONAL AND STRUCTURAL PROPERTIES. JRNL REF INT J MOL SCI V. 24 2023 JRNL REFN ESSN 1422-0067 JRNL PMID 38068946 JRNL DOI 10.3390/IJMS242316620 REMARK 2 REMARK 2 RESOLUTION. 1.22 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) : 1.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.420 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 3 NUMBER OF REFLECTIONS : 30355 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.590 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 41.6300 - 2.9300 0.99 2380 167 0.1681 0.1628 REMARK 3 2 2.9300 - 2.3200 0.99 2244 159 0.1470 0.2101 REMARK 3 3 2.3200 - 2.0300 0.98 2181 155 0.1246 0.1400 REMARK 3 4 2.0300 - 1.8500 0.98 2195 153 0.1265 0.1766 REMARK 3 5 1.8500 - 1.7100 0.97 2134 151 0.1210 0.1539 REMARK 3 6 1.7100 - 1.6100 0.96 2139 151 0.1097 0.1730 REMARK 3 7 1.6100 - 1.5300 0.97 2128 151 0.1266 0.1828 REMARK 3 8 1.5300 - 1.4600 0.96 2098 148 0.1189 0.1835 REMARK 3 9 1.4600 - 1.4100 0.97 2122 149 0.1206 0.1734 REMARK 3 10 1.4100 - 1.3600 0.96 2117 149 0.1195 0.1933 REMARK 3 11 1.3600 - 1.3200 0.95 2097 148 0.1313 0.1938 REMARK 3 12 1.3200 - 1.2800 0.84 1843 131 0.1668 0.2415 REMARK 3 13 1.2800 - 1.2500 0.70 1526 106 0.2143 0.3215 REMARK 3 14 1.2500 - 1.2200 0.53 1151 82 0.2696 0.3338 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.540 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 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 : 0.024 1176 REMARK 3 ANGLE : 1.763 1572 REMARK 3 CHIRALITY : 0.123 153 REMARK 3 PLANARITY : 0.016 218 REMARK 3 DIHEDRAL : 14.680 480 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 8UQR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1000278065. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : 7B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30355 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.220 REMARK 200 RESOLUTION RANGE LOW (A) : 41.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.04487 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.26 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 1500, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 296K 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 15.48650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.82800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.21850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.82800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.48650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.21850 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 H SER B 325 O HOH B 401 1.46 REMARK 500 HG SER A 325 O HOH A 401 1.54 REMARK 500 HG3 MET B 340 O HOH C 445 1.55 REMARK 500 SD MET B 340 O HOH C 445 1.84 REMARK 500 CG MET B 340 O HOH C 445 1.98 REMARK 500 O HOH C 424 O HOH C 445 1.99 REMARK 500 O HOH C 416 O HOH C 438 2.07 REMARK 500 REMARK 500 REMARK: NULL 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 C 404 O HOH C 407 3645 2.13 REMARK 500 O HOH A 417 O HOH D 423 1455 2.14 REMARK 500 O HOH B 401 O HOH C 420 2654 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 ALA A 353 161.52 178.62 REMARK 500 GLN A 354 79.68 -100.72 REMARK 500 ALA C 355 65.03 32.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER A 325 -15.18 REMARK 500 SER A 325 -14.62 REMARK 500 REMARK 500 REMARK: NULL DBREF 8UQR A 326 356 UNP P04637 P53_HUMAN 326 356 DBREF 8UQR B 326 356 UNP P04637 P53_HUMAN 326 356 DBREF 8UQR C 326 356 UNP P04637 P53_HUMAN 326 356 DBREF 8UQR D 326 356 UNP P04637 P53_HUMAN 326 356 SEQADV 8UQR GLY A 324 UNP P04637 EXPRESSION TAG SEQADV 8UQR SER A 325 UNP P04637 EXPRESSION TAG SEQADV 8UQR GLY B 324 UNP P04637 EXPRESSION TAG SEQADV 8UQR SER B 325 UNP P04637 EXPRESSION TAG SEQADV 8UQR GLY C 324 UNP P04637 EXPRESSION TAG SEQADV 8UQR SER C 325 UNP P04637 EXPRESSION TAG SEQADV 8UQR GLY D 324 UNP P04637 EXPRESSION TAG SEQADV 8UQR SER D 325 UNP P04637 EXPRESSION TAG SEQRES 1 A 33 GLY SER GLU TYR PHE THR LEU GLN ILE ARG GLY ARG GLU SEQRES 2 A 33 ARG PHE GLU MET PHE ARG GLU LEU ASN GLU ALA LEU GLU SEQRES 3 A 33 LEU LYS ASP ALA GLN ALA GLY SEQRES 1 B 33 GLY SER GLU TYR PHE THR LEU GLN ILE ARG GLY ARG GLU SEQRES 2 B 33 ARG PHE GLU MET PHE ARG GLU LEU ASN GLU ALA LEU GLU SEQRES 3 B 33 LEU LYS ASP ALA GLN ALA GLY SEQRES 1 C 33 GLY SER GLU TYR PHE THR LEU GLN ILE ARG GLY ARG GLU SEQRES 2 C 33 ARG PHE GLU MET PHE ARG GLU LEU ASN GLU ALA LEU GLU SEQRES 3 C 33 LEU LYS ASP ALA GLN ALA GLY SEQRES 1 D 33 GLY SER GLU TYR PHE THR LEU GLN ILE ARG GLY ARG GLU SEQRES 2 D 33 ARG PHE GLU MET PHE ARG GLU LEU ASN GLU ALA LEU GLU SEQRES 3 D 33 LEU LYS ASP ALA GLN ALA GLY FORMUL 5 HOH *147(H2 O) HELIX 1 AA1 GLY A 334 LEU A 350 1 17 HELIX 2 AA2 GLY B 334 ALA B 353 1 20 HELIX 3 AA3 GLY C 334 ALA C 355 1 22 HELIX 4 AA4 GLY D 334 GLY D 356 1 23 SHEET 1 AA1 2 TYR A 327 ILE A 332 0 SHEET 2 AA1 2 PHE C 328 ARG C 333 -1 O PHE C 328 N ILE A 332 SHEET 1 AA2 2 PHE B 328 ARG B 333 0 SHEET 2 AA2 2 TYR D 327 ILE D 332 -1 O PHE D 328 N ILE B 332 CISPEP 1 ALA C 355 GLY C 356 0 10.89 CRYST1 30.973 56.437 61.656 90.00 90.00 90.00 P 21 21 21 16 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 0.032286 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017719 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016219 0.00000