PDB Short entry for 3IGL HEADER TRANSCRIPTION/DNA 28-JUL-09 3IGL TITLE DIVERSITY IN DNA RECOGNITION BY P53 REVEALED BY CRYSTAL STRUCTURES TITLE 2 WITH HOOGSTEEN BASE PAIRS (P53-DNA COMPLEX 1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULAR TUMOR ANTIGEN P53; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: P53 CORE DOMAIN, UNP RESIDUES 94-293; COMPND 5 SYNONYM: TUMOR SUPPRESSOR P53, PHOSPHOPROTEIN P53, ANTIGEN NY-CO-13; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3'); COMPND 9 CHAIN: B; COMPND 10 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET27-B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SYNTHETIC DNA FRAGMENT. KEYWDS P53, MUTANT PROTEIN, LOOP-SHEET-HELIX MOTIF, DNA TARGET, ACTIVATOR, KEYWDS 2 ANTI-ONCOGENE APOPTOSIS, CELL CYCLE, COVALENT PROTEIN-RNA LINKAGE, KEYWDS 3 DISEASE MUTATION, DNA-BINDING, ENDOPLASMIC RETICULUM, GLYCOPROTEIN, KEYWDS 4 HOST-VIRUS INTERACTION, LI-FRAUMENI SYNDROME, METAL-BINDING, KEYWDS 5 METHYLATION, NUCLEUS, PHOSPHOPROTEIN, TRANSCRIPTION, TRANSCRIPTION KEYWDS 6 REGULATION, TRANSCRIPTION/DNA COMPLE, APOPTOSIS, ISOPEPTIDE BOND, KEYWDS 7 TUMOR SUPPRESSOR, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.KITAYNER,O.SUAD,H.ROZENBERG,Z.SHAKKED REVDAT 4 01-NOV-23 3IGL 1 REMARK LINK REVDAT 3 08-JUN-11 3IGL 1 JRNL REVDAT 2 14-APR-10 3IGL 1 TITLE REVDAT 1 31-MAR-10 3IGL 0 JRNL AUTH M.KITAYNER,H.ROZENBERG,R.ROHS,O.SUAD,D.RABINOVICH,B.HONIG, JRNL AUTH 2 Z.SHAKKED JRNL TITL DIVERSITY IN DNA RECOGNITION BY P53 REVEALED BY CRYSTAL JRNL TITL 2 STRUCTURES WITH HOOGSTEEN BASE PAIRS JRNL REF NAT.STRUCT.MOL.BIOL. V. 17 423 2010 JRNL REFN ISSN 1545-9993 JRNL PMID 20364130 JRNL DOI 10.1038/NSMB.1800 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0078 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 19216 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1037 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1322 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.1750 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1539 REMARK 3 NUCLEIC ACID ATOMS : 225 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.90000 REMARK 3 B22 (A**2) : 0.30000 REMARK 3 B33 (A**2) : 0.52000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.60000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.123 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.132 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.438 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1852 ; 0.026 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2548 ; 2.347 ; 2.119 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 197 ; 6.815 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 74 ;37.025 ;21.757 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 274 ;12.294 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;16.153 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 278 ; 0.174 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1337 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 988 ; 2.767 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1611 ; 4.089 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 864 ; 5.525 ; 7.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 936 ; 7.231 ;10.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3IGL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054384. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-SEP-05 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC INC. MSC - BLUE CONFOCAL REMARK 200 MIRRORS REMARK 200 OPTICS : OSMIC INC. MSC-BLUE CONFOCAL REMARK 200 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 : 20255 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 29.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.22500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.300 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: 3IGK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.16M SODIUM ACETATE, 16% PEG 3350, PH REMARK 280 6.1, 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 68.58050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.92050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.58050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.92050 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: 3870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 -4.69083 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 67.76183 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 ASP A 184 REMARK 465 SER A 185 REMARK 465 ASP A 186 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 GLY A 226 O REMARK 470 LYS A 291 CE NZ REMARK 470 LYS A 292 CE NZ REMARK 470 DG B 12 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DG B 12 N9 C8 N7 C5 C6 O6 N1 REMARK 470 DG B 12 C2 N2 N3 C4 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 O HOH A 299 O HOH A 371 2.15 REMARK 500 O HOH A 298 O HOH A 372 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 163 CE1 TYR A 163 CZ 0.094 REMARK 500 DC B 1 C5' DC B 1 C4' 0.048 REMARK 500 DG B 3 C6 DG B 3 N1 0.042 REMARK 500 DG B 3 C8 DG B 3 N9 0.051 REMARK 500 DC B 5 C5' DC B 5 C4' 0.044 REMARK 500 DA B 6 C6 DA B 6 N1 0.056 REMARK 500 DG B 8 C2' DG B 8 C1' 0.065 REMARK 500 REMARK 500 REMARK: NULL 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 B 1 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 DC B 1 O4' - C1' - C2' ANGL. DEV. = 3.8 DEGREES REMARK 500 DC B 1 N1 - C1' - C2' ANGL. DEV. = 13.1 DEGREES REMARK 500 DC B 1 C6 - N1 - C2 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC B 1 C5 - C6 - N1 ANGL. DEV. = -3.3 DEGREES REMARK 500 DC B 1 N1 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 DC B 1 N3 - C2 - O2 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG B 2 C2 - N3 - C4 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG B 2 N7 - C8 - N9 ANGL. DEV. = -3.1 DEGREES REMARK 500 DG B 2 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DG B 3 O3' - P - OP2 ANGL. DEV. = 7.4 DEGREES REMARK 500 DG B 3 C6 - N1 - C2 ANGL. DEV. = -5.6 DEGREES REMARK 500 DG B 3 C5 - N7 - C8 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG B 3 N7 - C8 - N9 ANGL. DEV. = -4.2 DEGREES REMARK 500 DG B 4 C3' - C2' - C1' ANGL. DEV. = -6.5 DEGREES REMARK 500 DG B 4 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG B 4 C6 - N1 - C2 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG B 4 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG B 4 C4 - C5 - N7 ANGL. DEV. = -2.5 DEGREES REMARK 500 DG B 4 N3 - C2 - N2 ANGL. DEV. = -6.7 DEGREES REMARK 500 DC B 5 N3 - C4 - C5 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC B 5 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 DC B 5 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 DA B 6 C5' - C4' - O4' ANGL. DEV. = 6.9 DEGREES REMARK 500 DA B 6 N9 - C1' - C2' ANGL. DEV. = 11.6 DEGREES REMARK 500 DA B 6 O4' - C1' - N9 ANGL. DEV. = -13.1 DEGREES REMARK 500 DA B 6 C5 - N7 - C8 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT B 7 C5 - C6 - N1 ANGL. DEV. = -5.4 DEGREES REMARK 500 DC B 9 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 DC B 9 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 10 O4' - C1' - N1 ANGL. DEV. = -4.7 DEGREES REMARK 500 DC B 10 C6 - N1 - C2 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC B 10 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 DC B 11 O4' - C1' - C2' ANGL. DEV. = 3.9 DEGREES REMARK 500 DC B 11 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES 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 VAL A 225 -52.30 -26.84 REMARK 500 ARG A 248 -4.88 78.81 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 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 176 SG REMARK 620 2 HIS A 179 ND1 104.4 REMARK 620 3 CYS A 238 SG 108.3 113.6 REMARK 620 4 CYS A 242 SG 114.7 102.0 113.5 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 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 294 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IGK RELATED DB: PDB REMARK 900 RELATED ID: 3KZ8 RELATED DB: PDB DBREF 3IGL A 94 293 UNP P04637 P53_HUMAN 94 293 DBREF 3IGL B 1 12 PDB 3IGL 3IGL 1 12 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 SER 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 ARG 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 B 12 DC DG DG DG DC DA DT DG DC DC DC DG HET ZN A 1 1 HET EDO A 294 8 HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN ZN 2+ FORMUL 4 EDO C2 H6 O2 FORMUL 5 HOH *340(H2 O) HELIX 1 1 GLN A 165 MET A 169 5 5 HELIX 2 2 CYS A 176 CYS A 182 1 7 HELIX 3 3 CYS A 277 GLY A 293 1 17 SHEET 1 A 4 ARG A 110 GLY A 112 0 SHEET 2 A 4 CYS A 141 TRP A 146 -1 O GLN A 144 N GLY A 112 SHEET 3 A 4 THR A 230 TYR A 236 -1 O THR A 230 N LEU A 145 SHEET 4 A 4 ILE A 195 GLU A 198 -1 N ARG A 196 O ASN A 235 SHEET 1 B 7 CYS A 124 SER A 127 0 SHEET 2 B 7 LYS A 132 CYS 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 THR 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 LEU A 206 O SER A 215 LINK ZN ZN A 1 SG CYS A 176 1555 1555 2.34 LINK ZN ZN A 1 ND1 HIS A 179 1555 1555 2.02 LINK ZN ZN A 1 SG CYS A 238 1555 1555 2.32 LINK ZN ZN A 1 SG CYS A 242 1555 1555 2.35 SITE 1 AC1 4 CYS A 176 HIS A 179 CYS A 238 CYS A 242 SITE 1 AC2 7 HOH A 41 SER A 95 VAL A 97 GLY A 199 SITE 2 AC2 7 THR A 231 HIS A 233 HOH A 314 CRYST1 137.161 49.841 33.962 90.00 93.96 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 0.007291 0.000000 0.000505 0.00000 SCALE2 0.000000 0.020064 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029515 0.00000