HEADER TRANSCRIPTION 24-OCT-23 8UQS TITLE CRYSTAL STRUCTURE OF THE OPOSSUM P53 TETRAMERIZATION DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULAR TUMOR ANTIGEN P53 (FRAGMENT); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MONODELPHIS DOMESTICA; SOURCE 3 ORGANISM_COMMON: GRAY SHORT-TAILED OPOSSUM; SOURCE 4 ORGANISM_TAXID: 13616; SOURCE 5 GENE: P53; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OPOSSUM 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 8UQS 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. 1.35 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 3 NUMBER OF REFLECTIONS : 24002 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) : 0.169 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1992 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 32.3100 - 3.2500 1.00 1872 170 0.1850 0.2034 REMARK 3 2 3.2500 - 2.5800 1.00 1777 161 0.1663 0.1874 REMARK 3 3 2.5800 - 2.2600 1.00 1743 157 0.1517 0.1774 REMARK 3 4 2.2600 - 2.0500 1.00 1752 159 0.1383 0.1901 REMARK 3 5 2.0500 - 1.9000 1.00 1743 158 0.1482 0.1796 REMARK 3 6 1.9000 - 1.7900 1.00 1717 155 0.1440 0.2027 REMARK 3 7 1.7900 - 1.7000 1.00 1729 156 0.1447 0.1785 REMARK 3 8 1.7000 - 1.6300 1.00 1722 156 0.1592 0.2409 REMARK 3 9 1.6300 - 1.5600 1.00 1722 156 0.1773 0.2175 REMARK 3 10 1.5600 - 1.5100 0.99 1677 152 0.1844 0.2159 REMARK 3 11 1.5100 - 1.4600 0.93 1598 144 0.1962 0.2841 REMARK 3 12 1.4600 - 1.4200 0.80 1363 125 0.2525 0.3319 REMARK 3 13 1.4200 - 1.3800 0.61 1044 96 0.3355 0.3628 REMARK 3 14 1.3800 - 1.3500 0.32 551 47 0.3976 0.4303 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.350 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 : 0.010 1122 REMARK 3 ANGLE : 1.069 1498 REMARK 3 CHIRALITY : 0.069 156 REMARK 3 PLANARITY : 0.013 197 REMARK 3 DIHEDRAL : 13.988 454 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 8UQS 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_1000277998. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-20 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) : 1.0000 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 : 24100 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 32.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 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 (%): 32.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.5, 20% PEG 1000, VAPOR REMARK 280 DIFFUSION, HANGING 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 19.13750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.12000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.44350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.12000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.13750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.44350 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: 6670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 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 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 ARG A 33 REMARK 465 ARG B 33 REMARK 465 GLY C 1 REMARK 465 GLY D 1 REMARK 465 ARG D 33 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 NE2 HIS A 31 HE1 HIS B 31 1.54 REMARK 500 HH11 ARG D 19 O HOH D 102 1.56 REMARK 500 HH22 ARG A 14 OE1 GLU C 29 1.59 REMARK 500 O HOH B 106 O HOH B 126 1.67 REMARK 500 O HOH B 117 O HOH B 128 2.14 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 B 109 O HOH D 114 3644 1.89 REMARK 500 O HOH C 136 O HOH D 121 4454 2.12 REMARK 500 REMARK 500 REMARK: NULL DBREF 8UQS A 3 33 UNP Q8HY32 Q8HY32_MONDO 198 228 DBREF 8UQS B 3 33 UNP Q8HY32 Q8HY32_MONDO 198 228 DBREF 8UQS C 3 33 UNP Q8HY32 Q8HY32_MONDO 198 228 DBREF 8UQS D 3 33 UNP Q8HY32 Q8HY32_MONDO 198 228 SEQADV 8UQS GLY A 1 UNP Q8HY32 EXPRESSION TAG SEQADV 8UQS SER A 2 UNP Q8HY32 EXPRESSION TAG SEQADV 8UQS GLY B 1 UNP Q8HY32 EXPRESSION TAG SEQADV 8UQS SER B 2 UNP Q8HY32 EXPRESSION TAG SEQADV 8UQS GLY C 1 UNP Q8HY32 EXPRESSION TAG SEQADV 8UQS SER C 2 UNP Q8HY32 EXPRESSION TAG SEQADV 8UQS GLY D 1 UNP Q8HY32 EXPRESSION TAG SEQADV 8UQS SER D 2 UNP Q8HY32 EXPRESSION TAG SEQRES 1 A 33 GLY SER GLU TYR PHE THR LEU GLN ILE ARG GLY ARG GLN SEQRES 2 A 33 ARG TYR GLU LEU LEU ARG GLU ILE ASN GLU ALA LEU GLU SEQRES 3 A 33 LEU LYS GLU ALA HIS SER ARG SEQRES 1 B 33 GLY SER GLU TYR PHE THR LEU GLN ILE ARG GLY ARG GLN SEQRES 2 B 33 ARG TYR GLU LEU LEU ARG GLU ILE ASN GLU ALA LEU GLU SEQRES 3 B 33 LEU LYS GLU ALA HIS SER ARG SEQRES 1 C 33 GLY SER GLU TYR PHE THR LEU GLN ILE ARG GLY ARG GLN SEQRES 2 C 33 ARG TYR GLU LEU LEU ARG GLU ILE ASN GLU ALA LEU GLU SEQRES 3 C 33 LEU LYS GLU ALA HIS SER ARG SEQRES 1 D 33 GLY SER GLU TYR PHE THR LEU GLN ILE ARG GLY ARG GLN SEQRES 2 D 33 ARG TYR GLU LEU LEU ARG GLU ILE ASN GLU ALA LEU GLU SEQRES 3 D 33 LEU LYS GLU ALA HIS SER ARG FORMUL 5 HOH *133(H2 O) HELIX 1 AA1 GLY A 11 HIS A 31 1 21 HELIX 2 AA2 GLY B 11 HIS B 31 1 21 HELIX 3 AA3 GLY C 11 HIS C 31 1 21 HELIX 4 AA4 GLY D 11 SER D 32 1 22 SHEET 1 AA1 2 TYR A 4 ARG A 10 0 SHEET 2 AA1 2 TYR C 4 ARG C 10 -1 O ILE C 9 N PHE A 5 SHEET 1 AA2 2 TYR B 4 ARG B 10 0 SHEET 2 AA2 2 TYR D 4 ARG D 10 -1 O LEU D 7 N LEU B 7 CRYST1 38.275 50.887 60.240 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 0.026127 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019651 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016600 0.00000