HEADER HYDROLASE 22-OCT-10 3PDH TITLE STRUCTURE OF SIR2TM BOUND TO A PROPIONYLATED PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT DEACETYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: REGULATORY PROTEIN SIR2 HOMOLOG; COMPND 5 EC: 3.5.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CELLULAR TUMOR ANTIGEN P53 18-RESIDUE PEPTIDE; COMPND 9 CHAIN: D; COMPND 10 SYNONYM: ANTIGEN NY-CO-13, PHOSPHOPROTEIN P53, TUMOR SUPPRESSOR P53; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: NPDA, SIR2, TM_0490; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: T7 BASED INDUCIBLE VECTOR; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: CHEMICALLY SYNTHESIZED PROPIONYLATED P53 PEPTIDE KEYWDS ROSSMANN FOLD, DEACETYLASE, DEACYLASE, DEPROPIONYLASE, N6-PROPIONYL- KEYWDS 2 LYSINE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.WOLBERGER,P.BHEDA REVDAT 1 19-JAN-11 3PDH 0 JRNL AUTH P.BHEDA,J.T.WANG,J.C.ESCALANTE-SEMERENA,C.WOLBERGER JRNL TITL STRUCTURE OF SIR2TM BOUND TO A PROPIONYLATED PEPTIDE. JRNL REF PROTEIN SCI. V. 20 131 2011 JRNL REFN ISSN 0961-8368 JRNL PMID 21080423 JRNL DOI 10.1002/PRO.544 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON 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) : 30.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 26911 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1430 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) : 1931 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 104 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1958 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 247 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.63000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : -0.84000 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): 0.109 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.112 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.071 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.722 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2092 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1470 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2839 ; 1.612 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3616 ; 0.951 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 274 ; 6.757 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 93 ;34.892 ;24.301 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 402 ;13.696 ;15.012 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;20.086 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 325 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2306 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 408 ; 0.001 ; 0.020 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): 1285 ; 1.190 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 517 ; 0.443 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2094 ; 1.828 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 807 ; 2.869 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 731 ; 4.117 ; 4.500 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 43 A 74 REMARK 3 RESIDUE RANGE : A 119 A 163 REMARK 3 ORIGIN FOR THE GROUP (A): -4.5950 36.5570 14.3820 REMARK 3 T TENSOR REMARK 3 T11: 0.1278 T22: 0.0414 REMARK 3 T33: 0.0637 T12: -0.0109 REMARK 3 T13: 0.0023 T23: -0.0179 REMARK 3 L TENSOR REMARK 3 L11: 1.6918 L22: 3.3626 REMARK 3 L33: 5.6811 L12: -0.4190 REMARK 3 L13: 1.7289 L23: 1.2053 REMARK 3 S TENSOR REMARK 3 S11: -0.0871 S12: 0.0828 S13: 0.1569 REMARK 3 S21: -0.2668 S22: -0.0020 S23: -0.0493 REMARK 3 S31: -0.4401 S32: 0.2530 S33: 0.0891 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 33 REMARK 3 RESIDUE RANGE : A 76 A 117 REMARK 3 RESIDUE RANGE : A 165 A 246 REMARK 3 ORIGIN FOR THE GROUP (A): 2.8360 9.5270 10.2360 REMARK 3 T TENSOR REMARK 3 T11: 0.0192 T22: 0.0232 REMARK 3 T33: 0.0409 T12: -0.0093 REMARK 3 T13: -0.0002 T23: -0.0023 REMARK 3 L TENSOR REMARK 3 L11: 1.6503 L22: 1.6750 REMARK 3 L33: 2.6340 L12: -0.4182 REMARK 3 L13: -0.0570 L23: -0.2661 REMARK 3 S TENSOR REMARK 3 S11: -0.0281 S12: 0.0073 S13: -0.1013 REMARK 3 S21: 0.0078 S22: -0.0086 S23: -0.0400 REMARK 3 S31: 0.1435 S32: 0.0092 S33: 0.0367 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 2 D 14 REMARK 3 ORIGIN FOR THE GROUP (A): 4.8400 21.3310 29.9140 REMARK 3 T TENSOR REMARK 3 T11: 0.3025 T22: 0.2165 REMARK 3 T33: 0.1460 T12: 0.1222 REMARK 3 T13: -0.0316 T23: 0.0380 REMARK 3 L TENSOR REMARK 3 L11: 4.2001 L22: 9.1463 REMARK 3 L33: 26.8497 L12: 0.2941 REMARK 3 L13: -1.5811 L23: 1.7384 REMARK 3 S TENSOR REMARK 3 S11: -0.3090 S12: -0.8774 S13: -0.2533 REMARK 3 S21: 1.0673 S22: 0.1701 S23: -0.3801 REMARK 3 S31: 1.1522 S32: 1.0653 S33: 0.1389 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3PDH COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-NOV-10. REMARK 100 THE RCSB ID CODE IS RCSB062244. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9002 REMARK 200 MONOCHROMATOR : BENT GE(111) REMARK 200 OPTICS : BENT CONICAL SI-MIRROR (RH REMARK 200 COATED) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28346 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.8000 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) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.63900 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: MOLREP REMARK 200 STARTING MODEL: 2H4F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE OBTAINED FROM 1:1 MIX OF REMARK 280 PROTEIN AND THE WELL SOLUTION (9.5% (W/V) PEG3350, 100 MM CHES REMARK 280 BUFFER), PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 23.28050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.17250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.00650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.17250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.28050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.00650 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 34 REMARK 465 GLY A 35 REMARK 465 PRO A 36 REMARK 465 ASN A 37 REMARK 465 GLY A 38 REMARK 465 ILE A 39 REMARK 465 TYR A 40 REMARK 465 LYS A 41 REMARK 465 LYS A 42 REMARK 465 LYS D 1 REMARK 465 LYS D 15 REMARK 465 THR D 16 REMARK 465 GLU D 17 REMARK 465 GLY D 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 PHE A 33 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 45 CG CD OE1 NE2 REMARK 470 ARG A 62 CZ NH1 NH2 REMARK 470 GLU A 66 CG CD OE1 OE2 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 OE1 GLU A 241 O HOH A 394 4555 1.91 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 GLN A 45 -48.92 82.67 REMARK 500 ILE A 68 -56.97 -122.58 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 A 1 LYS A 2 141.33 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 105.5 REMARK 620 3 CYS A 151 SG 121.4 117.1 REMARK 620 4 CYS A 124 SG 108.0 106.9 96.5 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 1001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2H2F RELATED DB: PDB REMARK 900 SIR2TM BOUND TO P53 PEPTIDE REMARK 900 RELATED ID: 2H2D RELATED DB: PDB REMARK 900 SIR2TM BOUND TO ACETYLATED P53 PEPTIDE REMARK 900 RELATED ID: 2H4F RELATED DB: PDB REMARK 900 TERNARY COMPLEX OF SIR2TM BOUND TO ACETYLATED P53 AND NAD+ REMARK 900 RELATED ID: 2H4J RELATED DB: PDB REMARK 900 SIR2TM BOUND TO DEACETYLATED P53, NICOTINAMIDE, AND 2' REMARK 900 OAADPR FROM ENZYMATIC TURNOVER IN CRYSTAL DBREF 3PDH A 1 246 UNP Q9WYW0 NPD_THEMA 1 246 DBREF 3PDH D 1 18 UNP P04637 P53_HUMAN 372 389 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 HIS 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 D 18 LYS LYS GLY GLN SER THR SER ARG HIS LYS PRK LEU MET SEQRES 2 D 18 PHE LYS THR GLU GLY MODRES 3PDH PRK D 11 LYS N~6~-PROPANOYL-L-LYSINE HET PRK D 11 13 HET ZN A1001 1 HETNAM PRK N~6~-PROPANOYL-L-LYSINE HETNAM ZN ZINC ION HETSYN PRK N(6)-PROPIONYLLYSINE FORMUL 2 PRK C9 H18 N2 O3 FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *247(H2 O) HELIX 1 1 MET A 3 SER A 13 1 11 HELIX 2 2 GLY A 21 THR A 26 1 6 HELIX 3 3 PRO A 27 GLY A 29 5 3 HELIX 4 4 ASP A 49 HIS A 56 1 8 HELIX 5 5 HIS A 56 ILE A 68 1 13 HELIX 6 6 PHE A 69 ALA A 74 5 6 HELIX 7 7 ASN A 77 LYS A 89 1 13 HELIX 8 8 ARG A 102 ALA A 107 1 6 HELIX 9 9 VAL A 133 GLU A 141 1 9 HELIX 10 10 PRO A 167 ALA A 181 1 15 HELIX 11 11 PRO A 195 ALA A 197 5 3 HELIX 12 12 GLU A 198 GLY A 207 1 10 HELIX 13 13 PHE A 220 ALA A 224 5 5 HELIX 14 14 ASP A 231 GLY A 244 1 14 HELIX 15 15 GLY D 3 LYS D 10 5 8 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 187 N LEU A 19 SHEET 5 A 6 LYS A 209 VAL A 213 1 O VAL A 211 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 ASN A 158 N GLU A 121 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 LINK C LYS D 10 N PRK D 11 1555 1555 1.34 LINK C PRK D 11 N LEU D 12 1555 1555 1.33 LINK SG CYS A 127 ZN ZN A1001 1555 1555 2.17 LINK SG CYS A 148 ZN ZN A1001 1555 1555 2.31 LINK SG CYS A 151 ZN ZN A1001 1555 1555 2.33 LINK SG CYS A 124 ZN ZN A1001 1555 1555 2.40 CISPEP 1 ASP A 32 PHE A 33 0 29.93 CISPEP 2 TYR A 194 PRO A 195 0 2.38 SITE 1 AC1 4 CYS A 124 CYS A 127 CYS A 148 CYS A 151 CRYST1 46.561 60.013 106.345 90.00 90.00 90.00 P 21 21 21 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 0.021477 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016663 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009403 0.00000