HEADER HYDROLASE/LIGASE 25-JUN-13 4BVE TITLE CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THIOALKYLIMIDATE TITLE 2 FORMED FROM THIO-ACETYL-LYSINE ACS2-PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 116-399; COMPND 5 SYNONYM: HSIRT3, REGULATORY PROTEIN SIR2 HOMOLOG 3, SIR2-LIKE PROTEIN COMPND 6 3, SIRT3; COMPND 7 EC: 3.5.1.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: ACETYL-COENZYME A SYNTHETASE 2-LIKE, MITOCHONDRIAL; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: RESIDUES 640-645; COMPND 13 SYNONYM: THIO-ACETYL-LYSINE ACS2-PEPTIDE, ACETATE-COA LIGASE 2, COMPND 14 ACETYL-COA SYNTHETASE 2, ACECS2, ACYL-COA SYNTHETASE SHORT-CHAIN COMPND 15 FAMILY MEMBER 1; COMPND 16 EC: 6.2.1.1; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PVFT3S; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS HYDROLASE-LIGASE COMPLEX, THIO-INTERMEDIATE EXPDTA X-RAY DIFFRACTION AUTHOR M.GERTZ,M.WEYAND,C.STEEGBORN REVDAT 4 13-NOV-24 4BVE 1 REMARK REVDAT 3 20-DEC-23 4BVE 1 REMARK LINK REVDAT 2 07-AUG-13 4BVE 1 JRNL REVDAT 1 17-JUL-13 4BVE 0 JRNL AUTH M.GERTZ,F.FISCHER,G.T.T.NGUYEN,M.LAKSHMINARASIMHAN, JRNL AUTH 2 M.SCHUTKOWSKI,M.WEYAND,C.STEEGBORN JRNL TITL EX-527 INHIBITS SIRTUINS BY EXPLOITING THEIR UNIQUE JRNL TITL 2 NAD+-DEPENDENT DEACETYLATION MECHANISM JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 E2772 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 23840057 JRNL DOI 10.1073/PNAS.1303628110 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 23831 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) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1255 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1741 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.1900 REMARK 3 BIN FREE R VALUE SET COUNT : 92 REMARK 3 BIN FREE R VALUE : 0.2160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2231 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 221 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.12000 REMARK 3 B22 (A**2) : -0.33000 REMARK 3 B33 (A**2) : 0.46000 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): 0.146 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.142 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.089 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.224 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2391 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3275 ; 2.108 ; 2.017 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 305 ; 5.897 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;35.814 ;22.647 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 394 ;15.041 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;19.054 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 374 ; 0.142 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1805 ; 0.011 ; 0.022 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): 1146 ; 1.985 ; 1.821 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1435 ; 3.013 ; 2.704 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1242 ; 2.795 ; 2.082 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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.HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U REMARK 3 VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4BVE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1290057455. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918 REMARK 200 MONOCHROMATOR : SI(111) MONOCHROMATOR REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25087 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 34.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.57000 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3GLT REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.2 M LISO4, 0.1 M NA REMARK 280 CITRATE PH 5.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 38.24500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.24500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 40.49500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 63.48500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.49500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 63.48500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.24500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.49500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 63.48500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.24500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.49500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 63.48500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.8 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 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 GLY A 116 REMARK 465 SER A 117 REMARK 465 SER A 118 REMARK 465 ASP A 119 REMARK 465 LYS A 120 REMARK 465 ASP A 395 REMARK 465 GLY A 396 REMARK 465 PRO A 397 REMARK 465 ASP A 398 REMARK 465 LYS A 399 REMARK 465 THR B -2 REMARK 465 ARG B -1 REMARK 465 ARG B 6 REMARK 465 LEU B 7 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 ARG A 279 CD ARG A 279 NE -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 ARG A 158 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 279 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 279 NE - CZ - NH2 ANGL. DEV. = -8.6 DEGREES REMARK 500 ARG A 345 NE - CZ - NH2 ANGL. DEV. = -3.5 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 LYS A 122 87.80 -33.94 REMARK 500 ASN A 188 92.92 -162.09 REMARK 500 ARG A 224 147.49 -170.70 REMARK 500 VAL A 258 -64.29 -101.11 REMARK 500 ASP A 290 46.98 -75.16 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 A1395 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 256 SG REMARK 620 2 CYS A 259 SG 106.6 REMARK 620 3 CYS A 280 SG 108.1 110.0 REMARK 620 4 CYS A 283 SG 95.7 119.1 115.3 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 1395 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1396 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 1397 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1398 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1399 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BV2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SIR2 IN COMPLEX WITH EX-527 AND 2'-O-ACETYL- REMARK 900 ADP-RIBOSE REMARK 900 RELATED ID: 4BV3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SIRT3 IN COMPLEX WITH EX-527 AND NAD REMARK 900 RELATED ID: 4BVB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH EX- 527 AND ADP- REMARK 900 RIBOSE REMARK 900 RELATED ID: 4BVF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THIOALKYLIMIDATE REMARK 900 FORMED FROM THIO-ACETYL-LYSINE ACS2- PEPTIDE CRYSTALLIZED IN REMARK 900 PRESENCE OF THE INHIBITOR EX- 527 REMARK 900 RELATED ID: 4BVG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH NATIVE REMARK 900 ALKYLIMIDATE FORMED FROM ACETYL-LYSINE ACS2- PEPTIDE CRYSTALLIZED REMARK 900 IN PRESENCE OF THE INHIBITOR EX- 527 REMARK 900 RELATED ID: 4BVH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THE INHIBITOR EX- REMARK 900 527 AND 2'-O-ACETYL-ADP-RIBOSE REMARK 900 RELATED ID: 4BUZ RELATED DB: PDB REMARK 900 SIR2 COMPLEX STRUCTURE MIXTURE OF EX-527 INHIBITOR AND REACTION REMARK 900 PRODUCTS OR OF REACTION SUBSTRATES P53 PEPTIDE AND NAD REMARK 999 REMARK 999 SEQUENCE REMARK 999 CONSTRUCT COVERS RESIDUES 116-399 DBREF 4BVE A 116 399 UNP Q9NTG7 SIR3_HUMAN 116 399 DBREF 4BVE B -2 7 UNP Q9NUB1 ACS2L_HUMAN 638 647 SEQRES 1 A 284 GLY SER SER ASP LYS GLY LYS LEU SER LEU GLN ASP VAL SEQRES 2 A 284 ALA GLU LEU ILE ARG ALA ARG ALA CYS GLN ARG VAL VAL SEQRES 3 A 284 VAL MET VAL GLY ALA GLY ILE SER THR PRO SER GLY ILE SEQRES 4 A 284 PRO ASP PHE ARG SER PRO GLY SER GLY LEU TYR SER ASN SEQRES 5 A 284 LEU GLN GLN TYR ASP LEU PRO TYR PRO GLU ALA ILE PHE SEQRES 6 A 284 GLU LEU PRO PHE PHE PHE HIS ASN PRO LYS PRO PHE PHE SEQRES 7 A 284 THR LEU ALA LYS GLU LEU TYR PRO GLY ASN TYR LYS PRO SEQRES 8 A 284 ASN VAL THR HIS TYR PHE LEU ARG LEU LEU HIS ASP LYS SEQRES 9 A 284 GLY LEU LEU LEU ARG LEU TYR THR GLN ASN ILE ASP GLY SEQRES 10 A 284 LEU GLU ARG VAL SER GLY ILE PRO ALA SER LYS LEU VAL SEQRES 11 A 284 GLU ALA HIS GLY THR PHE ALA SER ALA THR CYS THR VAL SEQRES 12 A 284 CYS GLN ARG PRO PHE PRO GLY GLU ASP ILE ARG ALA ASP SEQRES 13 A 284 VAL MET ALA ASP ARG VAL PRO ARG CYS PRO VAL CYS THR SEQRES 14 A 284 GLY VAL VAL LYS PRO ASP ILE VAL PHE PHE GLY GLU PRO SEQRES 15 A 284 LEU PRO GLN ARG PHE LEU LEU HIS VAL VAL ASP PHE PRO SEQRES 16 A 284 MET ALA ASP LEU LEU LEU ILE LEU GLY THR SER LEU GLU SEQRES 17 A 284 VAL GLU PRO PHE ALA SER LEU THR GLU ALA VAL ARG SER SEQRES 18 A 284 SER VAL PRO ARG LEU LEU ILE ASN ARG ASP LEU VAL GLY SEQRES 19 A 284 PRO LEU ALA TRP HIS PRO ARG SER ARG ASP VAL ALA GLN SEQRES 20 A 284 LEU GLY ASP VAL VAL HIS GLY VAL GLU SER LEU VAL GLU SEQRES 21 A 284 LEU LEU GLY TRP THR GLU GLU MET ARG ASP LEU VAL GLN SEQRES 22 A 284 ARG GLU THR GLY LYS LEU ASP GLY PRO ASP LYS SEQRES 1 B 10 THR ARG SER GLY FZN VAL MET ARG ARG LEU MODRES 4BVE FZN B 2 LYS HET FZN B 2 47 HET ZN A1395 1 HET CL A1396 1 HET PEG A1397 7 HET SO4 A1398 5 HET EDO A1399 4 HETNAM FZN (2S)-2-AMINO-6-{[(1Z)-1-{[(2R,3R,4S,5R)-5-({[(R)-{[(R)- HETNAM 2 FZN {[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4- HETNAM 3 FZN DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY) HETNAM 4 FZN PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4- HETNAM 5 FZN DIHYDROXYTETRAHYDROFURAN-2- HETNAM 6 FZN YL]SULFANYL}ETHYLIDENE]AMINO}HEXANOIC ACID HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 FZN C23 H37 N7 O15 P2 S FORMUL 3 ZN ZN 2+ FORMUL 4 CL CL 1- FORMUL 5 PEG C4 H10 O3 FORMUL 6 SO4 O4 S 2- FORMUL 7 EDO C2 H6 O2 FORMUL 8 HOH *221(H2 O) HELIX 1 1 SER A 124 ALA A 134 1 11 HELIX 2 2 ALA A 146 GLY A 153 5 8 HELIX 3 3 GLY A 163 ASN A 167 5 5 HELIX 4 4 ASN A 167 ASP A 172 5 6 HELIX 5 5 TYR A 175 PHE A 180 5 6 HELIX 6 6 GLU A 181 ASN A 188 1 8 HELIX 7 7 PRO A 189 TYR A 200 1 12 HELIX 8 8 ASN A 207 LYS A 219 1 13 HELIX 9 9 GLY A 232 SER A 237 1 6 HELIX 10 10 PRO A 240 SER A 242 5 3 HELIX 11 11 ILE A 268 ALA A 274 1 7 HELIX 12 12 PRO A 299 LEU A 303 5 5 HELIX 13 13 LEU A 304 ALA A 312 1 9 HELIX 14 14 PHE A 327 VAL A 334 5 8 HELIX 15 15 VAL A 348 HIS A 354 1 7 HELIX 16 16 ASP A 365 GLY A 378 1 14 HELIX 17 17 TRP A 379 LEU A 394 1 16 SHEET 1 AA 6 LEU A 244 GLU A 246 0 SHEET 2 AA 6 LEU A 222 THR A 227 1 O LEU A 225 N VAL A 245 SHEET 3 AA 6 VAL A 140 VAL A 144 1 O VAL A 140 N LEU A 223 SHEET 4 AA 6 LEU A 314 LEU A 318 1 O LEU A 314 N VAL A 141 SHEET 5 AA 6 ARG A 340 ASN A 344 1 O LEU A 341 N ILE A 317 SHEET 6 AA 6 ASP A 359 LEU A 363 1 O VAL A 360 N LEU A 342 SHEET 1 AB 3 PRO A 262 PRO A 264 0 SHEET 2 AB 3 GLY A 249 CYS A 256 -1 O ALA A 254 N PHE A 263 SHEET 3 AB 3 VAL A 287 ILE A 291 -1 O LYS A 288 N THR A 255 SHEET 1 AC 2 VAL A 324 GLU A 325 0 SHEET 2 AC 2 VAL B 3 MET B 4 -1 O VAL B 3 N GLU A 325 LINK C GLY B 1 N FZN B 2 1555 1555 1.33 LINK C FZN B 2 N VAL B 3 1555 1555 1.34 LINK SG CYS A 256 ZN ZN A1395 1555 1555 2.40 LINK SG CYS A 259 ZN ZN A1395 1555 1555 2.37 LINK SG CYS A 280 ZN ZN A1395 1555 1555 2.25 LINK SG CYS A 283 ZN ZN A1395 1555 1555 2.22 CISPEP 1 GLU A 325 PRO A 326 0 1.70 SITE 1 AC1 4 CYS A 256 CYS A 259 CYS A 280 CYS A 283 SITE 1 AC2 1 GLN A 300 SITE 1 AC3 4 ASP A 267 GLY A 364 ASP A 365 HIS A 368 SITE 1 AC4 4 VAL A 277 ARG A 279 ARG A 384 HOH A2062 SITE 1 AC5 1 HIS A 187 CRYST1 80.990 126.970 76.490 90.00 90.00 90.00 C 2 2 21 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 0.012347 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007876 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013074 0.00000