HEADER APOPTOSIS/DNA 21-JUL-05 2ADY TITLE STRUCTURAL BASIS OF DNA RECOGNITION BY P53 TETRAMERS (COMPLEX IV) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*G)-3'; COMPND 3 CHAIN: E, F; COMPND 4 SYNONYM: TUMOR SUPPRESSOR P53, PHOSPHOPROTEIN P53, ANTIGEN NY-CO-13; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: CELLULAR TUMOR ANTIGEN P53; COMPND 8 CHAIN: A, B; COMPND 9 FRAGMENT: RESIDUES 94-293; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 5 ORGANISM_COMMON: HUMAN; SOURCE 6 ORGANISM_TAXID: 9606; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET27B KEYWDS PROTEIN-DNA COMPLEXES, APOPTOSIS-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.KITAYNER,H.ROZENBERG,N.KESSLER,D.RABINOVICH,Z.SHAKKED REVDAT 3 25-OCT-23 2ADY 1 REMARK REVDAT 2 24-FEB-09 2ADY 1 VERSN REVDAT 1 11-JUL-06 2ADY 0 JRNL AUTH M.KITAYNER,H.ROZENBERG,N.KESSLER,D.RABINOVICH,L.SHAULOV, JRNL AUTH 2 T.E.HARAN,Z.SHAKKED JRNL TITL STRUCTURAL BASIS OF DNA RECOGNITION BY P53 TETRAMERS JRNL REF MOL.CELL V. 22 741 2006 JRNL REFN ISSN 1097-2765 JRNL PMID 16793544 JRNL DOI 10.1016/J.MOLCEL.2006.05.015 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 15517 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 773 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 973 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.02 REMARK 3 BIN R VALUE (WORKING SET) : 0.1840 REMARK 3 BIN FREE R VALUE SET COUNT : 51 REMARK 3 BIN FREE R VALUE : 0.3140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3088 REMARK 3 NUCLEIC ACID ATOMS : 486 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 213 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.77000 REMARK 3 B22 (A**2) : -0.68000 REMARK 3 B33 (A**2) : 1.30000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.44000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.327 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.236 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.455 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.882 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3706 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5126 ; 1.999 ; 2.128 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 395 ; 7.137 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 147 ;35.826 ;22.381 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 525 ;20.083 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;20.202 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 561 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2697 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1764 ; 0.237 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2407 ; 0.318 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 286 ; 0.222 ; 0.200 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): 76 ; 0.265 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 16 ; 0.273 ; 0.200 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): 2031 ; 2.412 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3217 ; 3.909 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2046 ; 5.961 ; 7.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1908 ; 8.094 ;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 2ADY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1000033779. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15517 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 38.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.44300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 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: PDB ENTRY 1TSR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM FLUORIDE, PEG 3350, PH 6.2, REMARK 280 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 45.99850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.95150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.99850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.95150 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: OCTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, 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 -3.88541 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 74.88827 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 94 REMARK 465 GLY A 293 REMARK 465 LYS B 292 REMARK 465 GLY B 293 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 ARG A 290 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 291 CG CD CE NZ REMARK 470 LYS A 292 CA C O CB CG CD CE REMARK 470 LYS A 292 NZ REMARK 470 LYS B 291 C O CB CG CD CE NZ 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 347 O HOH A 372 2.06 REMARK 500 C5' DA F 4 O HOH F 23 2.08 REMARK 500 O CYS A 229 O HOH A 347 2.11 REMARK 500 OE2 GLU B 258 O HOH B 360 2.11 REMARK 500 O ALA B 119 N SER B 121 2.12 REMARK 500 OP2 DG F 2 O HOH F 22 2.13 REMARK 500 O LEU A 265 O HOH A 351 2.15 REMARK 500 O HOH E 204 O HOH B 330 2.16 REMARK 500 O HOH B 366 O HOH B 367 2.17 REMARK 500 O HOH A 396 O HOH A 397 2.17 REMARK 500 ND1 HIS B 214 O HOH B 325 2.19 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 DG E 2 O3' DG E 2 C3' -0.059 REMARK 500 DT E 7 O3' DT E 7 C3' -0.072 REMARK 500 DG E 8 O3' DG E 8 C3' -0.041 REMARK 500 DC F 5 O3' DC F 5 C3' -0.058 REMARK 500 DA F 6 O3' DA F 6 C3' -0.043 REMARK 500 CYS B 182 CB CYS B 182 SG -0.108 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 E 1 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 DA E 4 O5' - C5' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 DA E 4 O4' - C1' - N9 ANGL. DEV. = 6.6 DEGREES REMARK 500 DC E 5 C1' - O4' - C4' ANGL. DEV. = -7.8 DEGREES REMARK 500 DC E 5 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 DC E 5 O4' - C1' - N1 ANGL. DEV. = 9.0 DEGREES REMARK 500 DA E 6 N9 - C1' - C2' ANGL. DEV. = 8.4 DEGREES REMARK 500 DA E 6 O4' - C1' - N9 ANGL. DEV. = -8.1 DEGREES REMARK 500 DT E 7 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 DT E 7 N3 - C2 - O2 ANGL. DEV. = -4.0 DEGREES REMARK 500 DG E 8 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 DG E 8 C4 - C5 - N7 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG E 8 N1 - C6 - O6 ANGL. DEV. = 4.3 DEGREES REMARK 500 DG E 8 C5 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 DG E 12 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 DC F 1 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG F 2 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG F 3 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG F 3 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA F 4 O4' - C1' - C2' ANGL. DEV. = 4.0 DEGREES REMARK 500 DA F 4 O4' - C1' - N9 ANGL. DEV. = 8.9 DEGREES REMARK 500 DC F 5 OP1 - P - OP2 ANGL. DEV. = 9.4 DEGREES REMARK 500 DC F 5 O5' - P - OP2 ANGL. DEV. = -8.6 DEGREES REMARK 500 DC F 5 O5' - C5' - C4' ANGL. DEV. = -9.1 DEGREES REMARK 500 DC F 5 C1' - O4' - C4' ANGL. DEV. = -9.2 DEGREES REMARK 500 DC F 5 C4' - C3' - O3' ANGL. DEV. = -15.1 DEGREES REMARK 500 DC F 5 O4' - C1' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 DT F 7 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 DT F 7 C3' - C2' - C1' ANGL. DEV. = -6.2 DEGREES REMARK 500 DT F 7 O4' - C1' - C2' ANGL. DEV. = -7.4 DEGREES REMARK 500 DT F 7 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG F 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT F 9 C4 - C5 - C7 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT F 9 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 DC F 10 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC F 10 N3 - C4 - C5 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC F 11 O4' - C1' - C2' ANGL. DEV. = 4.5 DEGREES REMARK 500 DC F 11 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG F 12 O4' - C1' - N9 ANGL. DEV. = 2.7 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 PRO A 152 -177.57 -67.44 REMARK 500 SER A 183 64.87 30.23 REMARK 500 GLU A 224 175.65 -58.07 REMARK 500 VAL A 225 98.96 -41.18 REMARK 500 ARG A 248 0.78 86.01 REMARK 500 SER B 116 -19.90 -142.04 REMARK 500 ALA B 119 87.70 -63.40 REMARK 500 LYS B 120 -34.04 -2.34 REMARK 500 PRO B 153 128.72 -25.98 REMARK 500 ASN B 210 -67.75 -91.35 REMARK 500 PRO B 223 -175.18 -53.35 REMARK 500 ASP B 259 -159.64 -68.52 REMARK 500 LEU B 265 -24.48 -141.72 REMARK 500 CYS B 277 78.50 -113.91 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 107.4 REMARK 620 3 CYS A 238 SG 105.0 110.2 REMARK 620 4 CYS A 242 SG 113.8 107.3 113.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 176 SG REMARK 620 2 HIS B 179 ND1 105.5 REMARK 620 3 CYS B 238 SG 108.8 102.6 REMARK 620 4 CYS B 242 SG 118.7 111.1 108.8 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 ZN B 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AC0 RELATED DB: PDB REMARK 900 TUMOR SUPPRESSOR PROTEIN P53/DNA COMPLEX (I) REMARK 900 RELATED ID: 2AHI RELATED DB: PDB REMARK 900 TUMOR SUPPRESSOR PROTEIN P53/DNA COMPLEX (III) REMARK 900 RELATED ID: 2ATA RELATED DB: PDB REMARK 900 TUMOR SUPPRESSOR PROTEIN P53/DNA COMPLEX (II) DBREF 2ADY A 94 293 UNP P04637 P53_HUMAN 94 293 DBREF 2ADY B 94 293 UNP P04637 P53_HUMAN 94 293 DBREF 2ADY E 1 12 PDB 2ADY 2ADY 1 12 DBREF 2ADY F 1 12 PDB 2ADY 2ADY 1 12 SEQRES 1 E 12 DC DG DG DA DC DA DT DG DT DC DC DG SEQRES 1 F 12 DC DG DG DA DC DA DT DG DT DC DC DG 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 200 SER SER SER VAL PRO SER GLN LYS THR TYR GLN GLY SER SEQRES 2 B 200 TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY THR ALA SEQRES 3 B 200 LYS SER VAL THR CYS THR TYR SER PRO ALA LEU ASN LYS SEQRES 4 B 200 MET PHE CYS GLN LEU ALA LYS THR CYS PRO VAL GLN LEU SEQRES 5 B 200 TRP VAL ASP SER THR PRO PRO PRO GLY THR ARG VAL ARG SEQRES 6 B 200 ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET THR GLU SEQRES 7 B 200 VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SER ASP SEQRES 8 B 200 SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE ARG VAL SEQRES 9 B 200 GLU GLY ASN LEU ARG VAL GLU TYR LEU ASP ASP ARG ASN SEQRES 10 B 200 THR PHE ARG HIS SER VAL VAL VAL PRO TYR GLU PRO PRO SEQRES 11 B 200 GLU VAL GLY SER ASP CYS THR THR ILE HIS TYR ASN TYR SEQRES 12 B 200 MET CYS ASN SER SER CYS MET GLY GLY MET ASN ARG ARG SEQRES 13 B 200 PRO ILE LEU THR ILE ILE THR LEU GLU ASP SER SER GLY SEQRES 14 B 200 ASN LEU LEU GLY ARG ASN SER PHE GLU VAL ARG VAL CYS SEQRES 15 B 200 ALA CYS PRO GLY ARG ASP ARG ARG THR GLU GLU GLU ASN SEQRES 16 B 200 LEU ARG LYS LYS GLY HET ZN A 1 1 HET ZN B 1 1 HETNAM ZN ZINC ION FORMUL 5 ZN 2(ZN 2+) FORMUL 7 HOH *213(H2 O) HELIX 1 1 CYS A 176 ARG A 181 1 6 HELIX 2 2 CYS A 277 ASN A 288 1 12 HELIX 3 3 CYS B 176 ARG B 181 1 6 HELIX 4 4 CYS B 277 ASN B 288 1 12 SHEET 1 A 4 ARG A 110 PHE A 113 0 SHEET 2 A 4 CYS A 141 TRP A 146 -1 O TRP A 146 N ARG A 110 SHEET 3 A 4 THR A 230 TYR A 236 -1 O ILE A 232 N VAL A 143 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 PHE A 134 N THR A 125 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 ARG A 158 O THR A 256 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 SHEET 1 C 4 ARG B 110 GLY B 112 0 SHEET 2 C 4 CYS B 141 TRP B 146 -1 O GLN B 144 N GLY B 112 SHEET 3 C 4 CYS B 229 TYR B 236 -1 O THR B 230 N LEU B 145 SHEET 4 C 4 ILE B 195 VAL B 197 -1 N ARG B 196 O ASN B 235 SHEET 1 D 7 CYS B 124 SER B 127 0 SHEET 2 D 7 LYS B 132 CYS B 135 -1 O PHE B 134 N THR B 125 SHEET 3 D 7 LEU B 264 VAL B 274 1 O GLU B 271 N MET B 133 SHEET 4 D 7 ILE B 251 GLU B 258 -1 N ILE B 251 O VAL B 272 SHEET 5 D 7 ARG B 156 TYR B 163 -1 N MET B 160 O ILE B 254 SHEET 6 D 7 HIS B 214 PRO B 219 -1 O VAL B 218 N VAL B 157 SHEET 7 D 7 GLU B 204 ASP B 207 -1 N GLU B 204 O VAL B 217 LINK ZN ZN A 1 SG CYS A 176 1555 1555 2.41 LINK ZN ZN A 1 ND1 HIS A 179 1555 1555 2.10 LINK ZN ZN A 1 SG CYS A 238 1555 1555 2.31 LINK ZN ZN A 1 SG CYS A 242 1555 1555 2.29 LINK ZN ZN B 1 SG CYS B 176 1555 1555 2.47 LINK ZN ZN B 1 ND1 HIS B 179 1555 1555 2.08 LINK ZN ZN B 1 SG CYS B 238 1555 1555 2.23 LINK ZN ZN B 1 SG CYS B 242 1555 1555 2.27 SITE 1 AC1 4 CYS A 176 HIS A 179 CYS A 238 CYS A 242 SITE 1 AC2 4 CYS B 176 HIS B 179 CYS B 238 CYS B 242 CRYST1 91.997 67.903 74.989 90.00 92.97 90.00 C 1 2 1 8 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 0.010870 0.000000 0.000560 0.00000 SCALE2 0.000000 0.014730 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013350 0.00000