HEADER HYDROLASE 13-MAY-13 4BN4 TITLE STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH ADP-RIBOSE 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; COMPND 7 EC: 3.5.1.-; COMPND 8 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 KEYWDS HYDROLASE, LYSINE DEACETYLASE, ADP RIBOSE EXPDTA X-RAY DIFFRACTION AUTHOR G.T.T.NGUYEN,S.SCHAEFER,M.GERTZ,M.WEYAND,C.STEEGBORN REVDAT 7 20-DEC-23 4BN4 1 REMARK HETSYN LINK REVDAT 6 28-AUG-13 4BN4 1 ATOM ANISOU REVDAT 5 14-AUG-13 4BN4 1 ATOM ANISOU REVDAT 4 07-AUG-13 4BN4 1 ANISOU ATOM REVDAT 3 31-JUL-13 4BN4 1 JRNL REVDAT 2 24-JUL-13 4BN4 1 ATOM ANISOU REVDAT 1 26-JUN-13 4BN4 0 JRNL AUTH G.T.T.NGUYEN,S.SCHAEFER,M.GERTZ,M.WEYAND,C.STEEGBORN JRNL TITL STRUCTURES OF HUMAN SIRTUIN 3 COMPLEXES WITH ADP-RIBOSE AND JRNL TITL 2 WITH CARBA-NAD+ AND SRT1720: BINDING DETAILS AND INHIBITION JRNL TITL 3 MECHANISM JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 69 1423 2013 JRNL REFN ISSN 0907-4449 JRNL PMID 23897466 JRNL DOI 10.1107/S0907444913015448 REMARK 2 REMARK 2 RESOLUTION. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 66216 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) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3485 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4746 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.3080 REMARK 3 BIN FREE R VALUE SET COUNT : 249 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2124 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 266 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.91000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.94000 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): 0.045 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.047 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.035 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.958 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.981 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.972 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2373 ; 0.021 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2304 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3264 ; 2.192 ; 2.012 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5319 ; 1.249 ; 3.005 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 307 ; 6.170 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 104 ;33.529 ;22.788 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 382 ;11.835 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;20.217 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 373 ; 0.139 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2651 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 543 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 4677 ; 6.036 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 78 ;31.321 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4786 ;11.667 ; 5.000 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 4BN4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1290056850. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 0.91841 REMARK 200 MONOCHROMATOR : SI(111) MONOCHROMATOR REMARK 200 OPTICS : DYNAMICALLY BENDABLE MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69702 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 1.36000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 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 4FVT REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (V/V) PEG600, 5%(W/V) PEG1000, 10% REMARK 280 (V/V) GLYCEROL, 0.1 M MES, PH 6.0 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 31.95000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.42500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.33500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.42500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.95000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.33500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 LYS A 393 REMARK 465 LEU A 394 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 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 LYS A 190 CE NZ REMARK 470 ARG A 261 CD NE CZ NH1 NH2 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 HH22 ARG A 345 O HOH A 2219 1.35 REMARK 500 HE2 HIS A 305 O HOH A 2191 1.59 REMARK 500 O HOH A 2070 O HOH A 2162 1.80 REMARK 500 O HOH A 2020 O HOH A 2108 2.05 REMARK 500 OH TYR A 171 O HOH A 2044 2.12 REMARK 500 CZ TYR A 171 O HOH A 2044 2.16 REMARK 500 NH2 ARG A 345 O HOH A 2219 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 HG3 MET A 311 O HOH A 2044 2554 1.30 REMARK 500 O HOH A 2021 O HOH A 2045 2554 2.06 REMARK 500 O HOH A 2039 O HOH A 2110 2555 2.13 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 139 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 TYR A 211 CB - CG - CD1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 345 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 MET A 383 CG - SD - CE ANGL. DEV. = -11.7 DEGREES REMARK 500 ARG A 389 NE - CZ - NH1 ANGL. DEV. = 3.0 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 ASN A 188 100.62 -162.06 REMARK 500 VAL A 258 -60.88 -99.45 REMARK 500 THR A 284 -1.87 75.66 REMARK 500 ASP A 290 46.93 -75.72 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 NA A1394 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 149 OG REMARK 620 2 HIS A 210 NE2 68.7 REMARK 620 3 ASN A 229 OD1 75.7 122.5 REMARK 620 4 ASP A 231 OD1 88.5 117.7 104.6 REMARK 620 5 GLU A 234 OE2 155.6 111.5 84.9 111.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1393 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 256 SG REMARK 620 2 CYS A 259 SG 100.4 REMARK 620 3 CYS A 280 SG 109.5 110.8 REMARK 620 4 CYS A 283 SG 97.1 116.4 119.5 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 1393 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1394 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AR6 A 1395 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OP2 A 1396 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BN5 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH INHIBITOR DBREF 4BN4 A 116 399 UNP Q9NTG7 SIR3_HUMAN 116 399 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 HET ZN A1393 1 HET NA A1394 1 HET AR6 A1395 57 HET OP2 A1396 42 HETNAM ZN ZINC ION HETNAM NA SODIUM ION HETNAM AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY- HETNAM 2 AR6 OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5- HETNAM 3 AR6 TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN HETNAM 4 AR6 PHOSPHATE HETNAM OP2 2-[2-[2-[2-[2-(2-HYDROXYETHYLOXY) HETNAM 2 OP2 ETHOXY]ETHOXY]ETHOXY]ETHOXY]ETHANOIC ACID HETSYN AR6 ADENOSINE-5-DIPHOSPHORIBOSE FORMUL 2 ZN ZN 2+ FORMUL 3 NA NA 1+ FORMUL 4 AR6 C15 H23 N5 O14 P2 FORMUL 5 OP2 C12 H24 O8 FORMUL 6 HOH *266(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 GLN A 169 1 7 HELIX 4 4 TYR A 175 PHE A 180 5 6 HELIX 5 5 GLU A 181 ASN A 188 1 8 HELIX 6 6 PRO A 189 TYR A 200 1 12 HELIX 7 7 ASN A 207 LYS A 219 1 13 HELIX 8 8 GLY A 232 SER A 237 1 6 HELIX 9 9 PRO A 240 SER A 242 5 3 HELIX 10 10 GLY A 265 ALA A 274 1 10 HELIX 11 11 PRO A 299 LEU A 303 5 5 HELIX 12 12 LEU A 304 ALA A 312 1 9 HELIX 13 13 PRO A 326 THR A 331 1 6 HELIX 14 14 VAL A 348 HIS A 354 1 7 HELIX 15 15 ASP A 365 GLY A 378 1 14 HELIX 16 16 TRP A 379 GLY A 392 1 14 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 LINK OG SER A 149 NA NA A1394 1555 1555 3.04 LINK NE2 HIS A 210 NA NA A1394 1555 1555 2.95 LINK OD1 ASN A 229 NA NA A1394 1555 1555 2.94 LINK OD1 ASP A 231 NA NA A1394 1555 1555 2.72 LINK OE2 GLU A 234 NA NA A1394 1555 1555 2.77 LINK SG CYS A 256 ZN ZN A1393 1555 1555 2.34 LINK SG CYS A 259 ZN ZN A1393 1555 1555 2.21 LINK SG CYS A 280 ZN ZN A1393 1555 1555 2.28 LINK SG CYS A 283 ZN ZN A1393 1555 1555 2.24 CISPEP 1 GLU A 325 PRO A 326 0 5.53 SITE 1 AC1 4 CYS A 256 CYS A 259 CYS A 280 CYS A 283 SITE 1 AC2 5 SER A 149 HIS A 210 ASN A 229 ASP A 231 SITE 2 AC2 5 GLU A 234 SITE 1 AC3 24 GLY A 145 ALA A 146 GLY A 147 THR A 150 SITE 2 AC3 24 ASP A 156 PHE A 157 ARG A 158 TYR A 165 SITE 3 AC3 24 GLN A 228 HIS A 248 GLY A 319 THR A 320 SITE 4 AC3 24 SER A 321 VAL A 324 ASN A 344 ARG A 345 SITE 5 AC3 24 GLY A 364 ASP A 365 VAL A 366 HOH A2023 SITE 6 AC3 24 HOH A2032 HOH A2198 HOH A2222 HOH A2267 SITE 1 AC4 11 PRO A 155 PHE A 157 LEU A 168 TYR A 171 SITE 2 AC4 11 PRO A 191 ASN A 229 ILE A 230 ASP A 231 SITE 3 AC4 11 VAL A 306 MET A 311 HOH A2024 CRYST1 63.900 66.670 66.850 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 0.015649 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014999 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014959 0.00000