PDB Short entry for 2H59 HEADER HYDROLASE 25-MAY-06 2H59 TITLE SIR2 H116A-DEACETYLATED P53 PEPTIDE-3'-O-ACETYL ADP RIBOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT DEACETYLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: REGULATORY PROTEIN SIR2 HOMOLOG; COMPND 5 EC: 3.5.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: CELLULAR TUMOR ANTIGEN P53; COMPND 10 CHAIN: D, E; COMPND 11 SYNONYM: TUMOR SUPPRESSOR P53, PHOSPHOPROTEIN P53, ANTIGEN NY-CO-13; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: NPDA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET11A; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: FMOC SYNTHESIZED PEPTIDE KEYWDS ROSSMANN FOLD, ZN BINDING DOMAIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.G.HOFF,J.L.AVALOS,K.SENS,C.WOLBERGER REVDAT 5 30-AUG-23 2H59 1 REMARK REVDAT 4 20-OCT-21 2H59 1 REMARK SEQADV LINK REVDAT 3 31-JAN-18 2H59 1 REMARK REVDAT 2 24-FEB-09 2H59 1 VERSN REVDAT 1 05-SEP-06 2H59 0 JRNL AUTH K.G.HOFF,J.L.AVALOS,K.SENS,C.WOLBERGER JRNL TITL INSIGHTS INTO THE SIRTUIN MECHANISM FROM TERNARY COMPLEXES JRNL TITL 2 CONTAINING NAD(+) AND ACETYLATED PEPTIDE. JRNL REF STRUCTURE V. 14 1231 2006 JRNL REFN ISSN 0969-2126 JRNL PMID 16905097 JRNL DOI 10.1016/J.STR.2006.06.006 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 40570 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2164 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3006 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 173 REMARK 3 BIN FREE R VALUE : 0.3380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3952 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 77 REMARK 3 SOLVENT ATOMS : 215 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.48000 REMARK 3 B22 (A**2) : 0.48000 REMARK 3 B33 (A**2) : -0.96000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.169 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.156 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.109 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.675 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4109 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5561 ; 1.935 ; 2.013 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 500 ; 6.342 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 171 ;35.883 ;24.152 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 736 ;16.002 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;18.145 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 635 ; 0.152 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3004 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2025 ; 0.234 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2833 ; 0.315 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 268 ; 0.164 ; 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): 59 ; 0.259 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.247 ; 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): 2598 ; 1.186 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4053 ; 1.860 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1717 ; 2.835 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1508 ; 4.419 ; 4.500 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 : 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 2H59 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000037945. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BLU-ICE REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42803 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 30.6000 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 <I/SIGMA(I)> 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY: 1YC5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, NA-TARTRATE:K-PHOSPHATE, REMARK 280 NACL, NAD, PH 5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 100K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 128.54050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 64.27025 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 192.81075 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: 5690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, E 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 LYS D 1 REMARK 465 LYS D 2 REMARK 465 GLY D 3 REMARK 465 GLN D 4 REMARK 465 SER D 5 REMARK 465 THR D 6 REMARK 465 SER D 7 REMARK 465 ARG D 8 REMARK 465 LYS D 15 REMARK 465 THR D 16 REMARK 465 GLU D 17 REMARK 465 GLY D 18 REMARK 465 LYS E 1 REMARK 465 LYS E 2 REMARK 465 GLY E 3 REMARK 465 GLN E 4 REMARK 465 SER E 5 REMARK 465 THR E 6 REMARK 465 SER E 7 REMARK 465 ARG E 8 REMARK 465 LYS E 15 REMARK 465 THR E 16 REMARK 465 GLU E 17 REMARK 465 GLY E 18 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 ASN A 37 CG OD1 ND2 REMARK 470 GLU A 66 CG CD OE1 OE2 REMARK 470 GLN A 73 CG CD OE1 NE2 REMARK 470 ASN B 37 CG OD1 ND2 REMARK 470 GLU B 66 CG CD OE1 OE2 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 ILE B 245 OG SER B 246 1.77 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 MET A 184 CG MET A 184 SD -0.177 REMARK 500 GLU B 217 CG GLU B 217 CD 0.091 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 LYS A 2 23.28 -0.14 REMARK 500 MET A 3 -36.91 73.73 REMARK 500 ILE A 68 -60.18 -133.52 REMARK 500 ARG A 102 14.59 59.00 REMARK 500 ASP A 150 -60.45 -93.48 REMARK 500 ILE B 68 -60.52 -133.57 REMARK 500 ARG B 102 19.27 58.23 REMARK 500 SER B 142 -84.67 -96.08 REMARK 500 CYS B 151 -6.79 -141.81 REMARK 500 ILE B 245 111.66 88.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 MET E 13 PHE E 14 132.39 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 A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 127 SG REMARK 620 2 CYS A 148 SG 161.9 REMARK 620 3 CYS A 151 SG 119.6 46.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 124 SG REMARK 620 2 CYS B 127 SG 117.3 REMARK 620 3 CYS B 148 SG 98.2 105.8 REMARK 620 4 CYS B 151 SG 80.7 131.3 116.3 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 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE APR A 252 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3OD B 253 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2H4F RELATED DB: PDB REMARK 900 SIR2-P53 PEPTIDE-NAD REMARK 900 RELATED ID: 2H4H RELATED DB: PDB REMARK 900 SIR2 H116Y-P53 PEPTIDE-NAD REMARK 900 RELATED ID: 2H4J RELATED DB: PDB REMARK 900 SIR2-DEACETYLATE P53 PEPTIDE (FROM ENZYMATIC TURNOVER IN CRYSTAL) DBREF 2H59 A 1 246 UNP Q9WYW0 NPD_THEMA 1 246 DBREF 2H59 B 1 246 UNP Q9WYW0 NPD_THEMA 1 246 DBREF 2H59 D 1 18 UNP Q9NP68 P53_HUMAN 372 389 DBREF 2H59 E 1 18 UNP Q9NP68 P53_HUMAN 372 389 SEQADV 2H59 ALA A 116 UNP Q9WYW0 HIS 116 ENGINEERED MUTATION SEQADV 2H59 ALA B 116 UNP Q9WYW0 HIS 116 ENGINEERED MUTATION SEQRES 1 A 246 MET LYS MET LYS GLU PHE LEU ASP LEU LEU ASN GLU SER SEQRES 2 A 246 ARG LEU THR VAL THR LEU THR GLY ALA GLY ILE SER THR SEQRES 3 A 246 PRO SER GLY ILE PRO ASP PHE ARG GLY PRO ASN GLY ILE SEQRES 4 A 246 TYR LYS LYS TYR SER GLN ASN VAL PHE ASP ILE ASP PHE SEQRES 5 A 246 PHE TYR SER HIS PRO GLU GLU PHE TYR ARG PHE ALA LYS SEQRES 6 A 246 GLU GLY ILE PHE PRO MET LEU GLN ALA LYS PRO ASN LEU SEQRES 7 A 246 ALA HIS VAL LEU LEU ALA LYS LEU GLU GLU LYS GLY LEU SEQRES 8 A 246 ILE GLU ALA VAL ILE THR GLN ASN ILE ASP ARG LEU HIS SEQRES 9 A 246 GLN ARG ALA GLY SER LYS LYS VAL ILE GLU LEU ALA GLY SEQRES 10 A 246 ASN VAL GLU GLU TYR TYR CYS VAL ARG CYS GLU LYS LYS SEQRES 11 A 246 TYR THR VAL GLU ASP VAL ILE LYS LYS LEU GLU SER SER SEQRES 12 A 246 ASP VAL PRO LEU CYS ASP ASP CYS ASN SER LEU ILE ARG SEQRES 13 A 246 PRO ASN ILE VAL PHE PHE GLY GLU ASN LEU PRO GLN ASP SEQRES 14 A 246 ALA LEU ARG GLU ALA ILE GLY LEU SER SER ARG ALA SER SEQRES 15 A 246 LEU MET ILE VAL LEU GLY SER SER LEU VAL VAL TYR PRO SEQRES 16 A 246 ALA ALA GLU LEU PRO LEU ILE THR VAL ARG SER GLY GLY SEQRES 17 A 246 LYS LEU VAL ILE VAL ASN LEU GLY GLU THR PRO PHE ASP SEQRES 18 A 246 ASP ILE ALA THR LEU LYS TYR ASN MET ASP VAL VAL GLU SEQRES 19 A 246 PHE ALA ARG ARG VAL MET GLU GLU GLY GLY ILE SER SEQRES 1 B 246 MET LYS MET LYS GLU PHE LEU ASP LEU LEU ASN GLU SER SEQRES 2 B 246 ARG LEU THR VAL THR LEU THR GLY ALA GLY ILE SER THR SEQRES 3 B 246 PRO SER GLY ILE PRO ASP PHE ARG GLY PRO ASN GLY ILE SEQRES 4 B 246 TYR LYS LYS TYR SER GLN ASN VAL PHE ASP ILE ASP PHE SEQRES 5 B 246 PHE TYR SER HIS PRO GLU GLU PHE TYR ARG PHE ALA LYS SEQRES 6 B 246 GLU GLY ILE PHE PRO MET LEU GLN ALA LYS PRO ASN LEU SEQRES 7 B 246 ALA HIS VAL LEU LEU ALA LYS LEU GLU GLU LYS GLY LEU SEQRES 8 B 246 ILE GLU ALA VAL ILE THR GLN ASN ILE ASP ARG LEU HIS SEQRES 9 B 246 GLN ARG ALA GLY SER LYS LYS VAL ILE GLU LEU ALA GLY SEQRES 10 B 246 ASN VAL GLU GLU TYR TYR CYS VAL ARG CYS GLU LYS LYS SEQRES 11 B 246 TYR THR VAL GLU ASP VAL ILE LYS LYS LEU GLU SER SER SEQRES 12 B 246 ASP VAL PRO LEU CYS ASP ASP CYS ASN SER LEU ILE ARG SEQRES 13 B 246 PRO ASN ILE VAL PHE PHE GLY GLU ASN LEU PRO GLN ASP SEQRES 14 B 246 ALA LEU ARG GLU ALA ILE GLY LEU SER SER ARG ALA SER SEQRES 15 B 246 LEU MET ILE VAL LEU GLY SER SER LEU VAL VAL TYR PRO SEQRES 16 B 246 ALA ALA GLU LEU PRO LEU ILE THR VAL ARG SER GLY GLY SEQRES 17 B 246 LYS LEU VAL ILE VAL ASN LEU GLY GLU THR PRO PHE ASP SEQRES 18 B 246 ASP ILE ALA THR LEU LYS TYR ASN MET ASP VAL VAL GLU SEQRES 19 B 246 PHE ALA ARG ARG VAL MET GLU GLU GLY GLY ILE SER SEQRES 1 D 18 LYS LYS GLY GLN SER THR SER ARG HIS LYS LYS LEU MET SEQRES 2 D 18 PHE LYS THR GLU GLY SEQRES 1 E 18 LYS LYS GLY GLN SER THR SER ARG HIS LYS LYS LEU MET SEQRES 2 E 18 PHE LYS THR GLU GLY HET ZN A1001 1 HET APR A 252 36 HET ZN B1001 1 HET 3OD B 253 39 HETNAM ZN ZINC ION HETNAM APR ADENOSINE-5-DIPHOSPHORIBOSE HETNAM 3OD (2S,3S,4R,5S)-2-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6- HETNAM 2 3OD AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2- HETNAM 3 3OD YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY) HETNAM 4 3OD PHOSPHORYL]OXY}METHYL)-4,5-DIHYDROXYTETRAHYDROFURAN-3- HETNAM 5 3OD YL ACETATE FORMUL 5 ZN 2(ZN 2+) FORMUL 6 APR C15 H23 N5 O14 P2 FORMUL 8 3OD C17 H25 N5 O15 P2 FORMUL 9 HOH *215(H2 O) HELIX 1 1 MET A 3 SER A 13 1 11 HELIX 2 2 ALA A 22 GLY A 29 5 8 HELIX 3 3 GLY A 38 LYS A 42 5 5 HELIX 4 4 SER A 44 PHE A 48 5 5 HELIX 5 5 ASP A 49 HIS A 56 1 8 HELIX 6 6 HIS A 56 ILE A 68 1 13 HELIX 7 7 PHE A 69 ALA A 74 5 6 HELIX 8 8 ASN A 77 LYS A 89 1 13 HELIX 9 9 ARG A 102 ALA A 107 1 6 HELIX 10 10 VAL A 133 LEU A 140 1 8 HELIX 11 11 PRO A 167 ALA A 181 1 15 HELIX 12 12 PRO A 195 ALA A 197 5 3 HELIX 13 13 GLU A 198 GLY A 207 1 10 HELIX 14 14 PHE A 220 ALA A 224 5 5 HELIX 15 15 ASP A 231 GLU A 242 1 12 HELIX 16 16 MET B 3 SER B 13 1 11 HELIX 17 17 ALA B 22 GLY B 29 5 8 HELIX 18 18 GLY B 38 LYS B 42 5 5 HELIX 19 19 SER B 44 PHE B 48 5 5 HELIX 20 20 ASP B 49 HIS B 56 1 8 HELIX 21 21 HIS B 56 ILE B 68 1 13 HELIX 22 22 PHE B 69 ALA B 74 5 6 HELIX 23 23 ASN B 77 LYS B 89 1 13 HELIX 24 24 ARG B 102 ALA B 107 1 6 HELIX 25 25 VAL B 133 LEU B 140 1 8 HELIX 26 26 PRO B 167 ALA B 181 1 15 HELIX 27 27 PRO B 195 ALA B 197 5 3 HELIX 28 28 GLU B 198 GLY B 207 1 10 HELIX 29 29 PHE B 220 ALA B 224 5 5 HELIX 30 30 ASP B 231 GLU B 242 1 12 SHEET 1 A 6 VAL A 112 GLU A 114 0 SHEET 2 A 6 ALA A 94 THR A 97 1 N VAL A 95 O ILE A 113 SHEET 3 A 6 THR A 16 THR A 20 1 N THR A 18 O ILE A 96 SHEET 4 A 6 LEU A 183 LEU A 187 1 O LEU A 183 N VAL A 17 SHEET 5 A 6 LYS A 209 VAL A 213 1 O VAL A 213 N VAL A 186 SHEET 6 A 6 LEU A 226 TYR A 228 1 O TYR A 228 N ILE A 212 SHEET 1 B 3 LYS A 130 THR A 132 0 SHEET 2 B 3 GLY A 117 CYS A 124 -1 N TYR A 122 O TYR A 131 SHEET 3 B 3 ILE A 155 ILE A 159 -1 O ARG A 156 N TYR A 123 SHEET 1 C 2 VAL A 193 TYR A 194 0 SHEET 2 C 2 LEU D 12 MET D 13 -1 O LEU D 12 N TYR A 194 SHEET 1 D 6 VAL B 112 GLU B 114 0 SHEET 2 D 6 ALA B 94 THR B 97 1 N THR B 97 O ILE B 113 SHEET 3 D 6 THR B 16 THR B 20 1 N THR B 18 O ILE B 96 SHEET 4 D 6 LEU B 183 LEU B 187 1 O ILE B 185 N LEU B 19 SHEET 5 D 6 LYS B 209 VAL B 213 1 O VAL B 213 N VAL B 186 SHEET 6 D 6 LEU B 226 TYR B 228 1 O TYR B 228 N ILE B 212 SHEET 1 E 3 LYS B 130 THR B 132 0 SHEET 2 E 3 GLY B 117 CYS B 124 -1 N TYR B 122 O TYR B 131 SHEET 3 E 3 ILE B 155 ILE B 159 -1 O ARG B 156 N TYR B 123 SHEET 1 F 2 VAL B 193 TYR B 194 0 SHEET 2 F 2 LEU E 12 MET E 13 -1 O LEU E 12 N TYR B 194 SSBOND 1 CYS A 124 CYS A 148 1555 1555 2.06 SSBOND 2 CYS A 148 CYS A 151 1555 1555 2.05 LINK SG CYS A 127 ZN ZN A1001 1555 1555 2.26 LINK SG CYS A 148 ZN ZN A1001 1555 1555 2.76 LINK SG CYS A 151 ZN ZN A1001 1555 1555 1.47 LINK SG CYS B 124 ZN ZN B1001 1555 1555 2.73 LINK SG CYS B 127 ZN ZN B1001 1555 1555 2.26 LINK SG CYS B 148 ZN ZN B1001 1555 1555 2.62 LINK SG CYS B 151 ZN ZN B1001 1555 1555 2.66 CISPEP 1 TYR A 194 PRO A 195 0 3.74 CISPEP 2 TYR B 194 PRO B 195 0 -0.65 SITE 1 AC1 4 CYS A 124 CYS A 127 CYS A 148 CYS A 151 SITE 1 AC2 4 CYS B 124 CYS B 127 CYS B 148 CYS B 151 SITE 1 AC3 27 GLY A 21 ALA A 22 GLY A 23 THR A 26 SITE 2 AC3 27 PRO A 27 ASP A 32 PHE A 33 ARG A 34 SITE 3 AC3 27 TYR A 40 GLN A 98 PHE A 162 GLY A 188 SITE 4 AC3 27 SER A 189 SER A 190 VAL A 193 ASN A 214 SITE 5 AC3 27 LEU A 215 MET A 230 ASP A 231 VAL A 232 SITE 6 AC3 27 HOH A1009 HOH A1042 HOH A1058 HOH A1064 SITE 7 AC3 27 HOH A1089 HOH A1102 LYS D 11 SITE 1 AC4 28 GLY B 21 ALA B 22 GLY B 23 THR B 26 SITE 2 AC4 28 PRO B 27 ASP B 32 PHE B 33 ARG B 34 SITE 3 AC4 28 TYR B 40 GLN B 98 ALA B 116 PHE B 162 SITE 4 AC4 28 GLY B 188 SER B 189 SER B 190 VAL B 193 SITE 5 AC4 28 ASN B 214 LEU B 215 MET B 230 ASP B 231 SITE 6 AC4 28 VAL B 232 HOH B1003 HOH B1006 HOH B1035 SITE 7 AC4 28 HOH B1053 HOH B1075 LYS E 11 HOH E 192 CRYST1 46.996 46.996 257.081 90.00 90.00 90.00 P 41 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 0.021278 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021278 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003890 0.00000