HEADER HYDROLASE 14-APR-11 3RIY TITLE SIRT5 IS AN NAD-DEPENDENT PROTEIN LYSINE DEMALONYLASE AND TITLE 2 DESUCCINYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT DEACETYLASE SIRTUIN-5; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 34-302; COMPND 5 SYNONYM: SIR2-LIKE PROTEIN 5; COMPND 6 EC: 3.5.1.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PEPTIDE OF HISTONE 3 N-SUCCINYL LYSINE 9; COMPND 10 CHAIN: C, D; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SIR2L5, SIRT5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 R2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDEST-F1; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: HISTONE 3 (RESIDUE 4-15) WAS CHEMICALLY SYNTHESIZED. KEYWDS DESUCCINYLASE, DEMALONYLASE, POSTTRANSLATIONAL MODIFICATION, ZN- KEYWDS 2 BINDING DOMAIN, ROSSMANN FOLD DOMAIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHOU,Q.HAO REVDAT 4 01-NOV-23 3RIY 1 REMARK SEQADV LINK REVDAT 3 08-NOV-17 3RIY 1 REMARK REVDAT 2 11-APR-12 3RIY 1 JRNL REVDAT 1 23-NOV-11 3RIY 0 JRNL AUTH J.DU,Y.ZHOU,X.SU,J.J.YU,S.KHAN,H.JIANG,J.KIM,J.WOO,J.H.KIM, JRNL AUTH 2 B.H.CHOI,B.HE,W.CHEN,S.ZHANG,R.A.CERIONE,J.AUWERX,Q.HAO, JRNL AUTH 3 H.LIN JRNL TITL SIRT5 IS A NAD-DEPENDENT PROTEIN LYSINE DEMALONYLASE AND JRNL TITL 2 DESUCCINYLASE JRNL REF SCIENCE V. 334 806 2011 JRNL REFN ISSN 0036-8075 JRNL PMID 22076378 JRNL DOI 10.1126/SCIENCE.1207861 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 83691 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) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4177 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5669 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.1810 REMARK 3 BIN FREE R VALUE SET COUNT : 290 REMARK 3 BIN FREE R VALUE : 0.2560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4280 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 690 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.39000 REMARK 3 B22 (A**2) : 1.04000 REMARK 3 B33 (A**2) : -0.65000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.078 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.511 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4715 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6443 ; 2.027 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 611 ; 6.007 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 205 ;34.221 ;22.488 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 751 ;12.932 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;17.773 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 689 ; 0.140 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3660 ; 0.013 ; 0.021 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): 2884 ; 2.183 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4661 ; 3.088 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1831 ; 4.285 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1759 ; 6.031 ; 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): 4715 ; 2.497 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 692 ;10.516 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4569 ; 5.859 ; 3.000 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 : 1.40 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 3RIY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-APR-11. REMARK 100 THE DEPOSITION ID IS D_1000064988. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAY-09 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 : CHESS REMARK 200 BEAMLINE : F1 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83831 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.39800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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 3RIG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 4000, 6% GLYCEROL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 26.34550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.16050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.70850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 78.16050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.34550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.70850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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 30 REMARK 465 GLY B 30 REMARK 465 LYS C 4 REMARK 465 GLN C 5 REMARK 465 GLY C 13 REMARK 465 LYS C 14 REMARK 465 ALA C 15 REMARK 465 LYS D 4 REMARK 465 GLN D 5 REMARK 465 LYS D 14 REMARK 465 ALA D 15 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 690 O HOH B 481 2.01 REMARK 500 OE2 GLU B 123 O HOH B 687 2.15 REMARK 500 OE2 GLU A 123 O HOH A 651 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 GLU B 100 CD GLU B 100 OE2 0.086 REMARK 500 GLU B 107 CD GLU B 107 OE2 0.103 REMARK 500 GLU B 202 CD GLU B 202 OE2 0.073 REMARK 500 GLU B 277 CB GLU B 277 CG -0.116 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 127 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ASP A 196 CB - CG - OD1 ANGL. DEV. = 9.1 DEGREES REMARK 500 ASP A 196 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP A 228 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 267 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 267 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG B 119 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 127 NE - CZ - NH2 ANGL. DEV. = -3.4 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 ARG A 78 -134.32 48.81 REMARK 500 ASN A 94 68.01 -157.47 REMARK 500 ALA B 34 140.55 175.74 REMARK 500 ARG B 78 -133.52 49.92 REMARK 500 ASN B 94 67.24 -156.22 REMARK 500 CYS B 212 -82.98 -91.52 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 166 SG REMARK 620 2 CYS A 169 SG 108.4 REMARK 620 3 CYS A 207 SG 107.9 109.4 REMARK 620 4 CYS A 212 SG 104.8 117.2 108.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 166 SG REMARK 620 2 CYS B 169 SG 107.2 REMARK 620 3 CYS B 207 SG 106.3 112.3 REMARK 620 4 CYS B 212 SG 103.6 116.8 109.7 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 NAD A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 2002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RIG RELATED DB: PDB DBREF 3RIY A 34 302 UNP Q9NXA8 SIRT5_HUMAN 34 302 DBREF 3RIY B 34 302 UNP Q9NXA8 SIRT5_HUMAN 34 302 DBREF 3RIY C 4 15 PDB 3RIY 3RIY 4 15 DBREF 3RIY D 4 15 PDB 3RIY 3RIY 4 15 SEQADV 3RIY GLY A 30 UNP Q9NXA8 EXPRESSION TAG SEQADV 3RIY SER A 31 UNP Q9NXA8 EXPRESSION TAG SEQADV 3RIY PHE A 32 UNP Q9NXA8 EXPRESSION TAG SEQADV 3RIY THR A 33 UNP Q9NXA8 EXPRESSION TAG SEQADV 3RIY GLY B 30 UNP Q9NXA8 EXPRESSION TAG SEQADV 3RIY SER B 31 UNP Q9NXA8 EXPRESSION TAG SEQADV 3RIY PHE B 32 UNP Q9NXA8 EXPRESSION TAG SEQADV 3RIY THR B 33 UNP Q9NXA8 EXPRESSION TAG SEQRES 1 A 273 GLY SER PHE THR ALA ARG PRO SER SER SER MET ALA ASP SEQRES 2 A 273 PHE ARG LYS PHE PHE ALA LYS ALA LYS HIS ILE VAL ILE SEQRES 3 A 273 ILE SER GLY ALA GLY VAL SER ALA GLU SER GLY VAL PRO SEQRES 4 A 273 THR PHE ARG GLY ALA GLY GLY TYR TRP ARG LYS TRP GLN SEQRES 5 A 273 ALA GLN ASP LEU ALA THR PRO LEU ALA PHE ALA HIS ASN SEQRES 6 A 273 PRO SER ARG VAL TRP GLU PHE TYR HIS TYR ARG ARG GLU SEQRES 7 A 273 VAL MET GLY SER LYS GLU PRO ASN ALA GLY HIS ARG ALA SEQRES 8 A 273 ILE ALA GLU CYS GLU THR ARG LEU GLY LYS GLN GLY ARG SEQRES 9 A 273 ARG VAL VAL VAL ILE THR GLN ASN ILE ASP GLU LEU HIS SEQRES 10 A 273 ARG LYS ALA GLY THR LYS ASN LEU LEU GLU ILE HIS GLY SEQRES 11 A 273 SER LEU PHE LYS THR ARG CYS THR SER CYS GLY VAL VAL SEQRES 12 A 273 ALA GLU ASN TYR LYS SER PRO ILE CYS PRO ALA LEU SER SEQRES 13 A 273 GLY LYS GLY ALA PRO GLU PRO GLY THR GLN ASP ALA SER SEQRES 14 A 273 ILE PRO VAL GLU LYS LEU PRO ARG CYS GLU GLU ALA GLY SEQRES 15 A 273 CYS GLY GLY LEU LEU ARG PRO HIS VAL VAL TRP PHE GLY SEQRES 16 A 273 GLU ASN LEU ASP PRO ALA ILE LEU GLU GLU VAL ASP ARG SEQRES 17 A 273 GLU LEU ALA HIS CYS ASP LEU CYS LEU VAL VAL GLY THR SEQRES 18 A 273 SER SER VAL VAL TYR PRO ALA ALA MET PHE ALA PRO GLN SEQRES 19 A 273 VAL ALA ALA ARG GLY VAL PRO VAL ALA GLU PHE ASN THR SEQRES 20 A 273 GLU THR THR PRO ALA THR ASN ARG PHE ARG PHE HIS PHE SEQRES 21 A 273 GLN GLY PRO CYS GLY THR THR LEU PRO GLU ALA LEU ALA SEQRES 1 B 273 GLY SER PHE THR ALA ARG PRO SER SER SER MET ALA ASP SEQRES 2 B 273 PHE ARG LYS PHE PHE ALA LYS ALA LYS HIS ILE VAL ILE SEQRES 3 B 273 ILE SER GLY ALA GLY VAL SER ALA GLU SER GLY VAL PRO SEQRES 4 B 273 THR PHE ARG GLY ALA GLY GLY TYR TRP ARG LYS TRP GLN SEQRES 5 B 273 ALA GLN ASP LEU ALA THR PRO LEU ALA PHE ALA HIS ASN SEQRES 6 B 273 PRO SER ARG VAL TRP GLU PHE TYR HIS TYR ARG ARG GLU SEQRES 7 B 273 VAL MET GLY SER LYS GLU PRO ASN ALA GLY HIS ARG ALA SEQRES 8 B 273 ILE ALA GLU CYS GLU THR ARG LEU GLY LYS GLN GLY ARG SEQRES 9 B 273 ARG VAL VAL VAL ILE THR GLN ASN ILE ASP GLU LEU HIS SEQRES 10 B 273 ARG LYS ALA GLY THR LYS ASN LEU LEU GLU ILE HIS GLY SEQRES 11 B 273 SER LEU PHE LYS THR ARG CYS THR SER CYS GLY VAL VAL SEQRES 12 B 273 ALA GLU ASN TYR LYS SER PRO ILE CYS PRO ALA LEU SER SEQRES 13 B 273 GLY LYS GLY ALA PRO GLU PRO GLY THR GLN ASP ALA SER SEQRES 14 B 273 ILE PRO VAL GLU LYS LEU PRO ARG CYS GLU GLU ALA GLY SEQRES 15 B 273 CYS GLY GLY LEU LEU ARG PRO HIS VAL VAL TRP PHE GLY SEQRES 16 B 273 GLU ASN LEU ASP PRO ALA ILE LEU GLU GLU VAL ASP ARG SEQRES 17 B 273 GLU LEU ALA HIS CYS ASP LEU CYS LEU VAL VAL GLY THR SEQRES 18 B 273 SER SER VAL VAL TYR PRO ALA ALA MET PHE ALA PRO GLN SEQRES 19 B 273 VAL ALA ALA ARG GLY VAL PRO VAL ALA GLU PHE ASN THR SEQRES 20 B 273 GLU THR THR PRO ALA THR ASN ARG PHE ARG PHE HIS PHE SEQRES 21 B 273 GLN GLY PRO CYS GLY THR THR LEU PRO GLU ALA LEU ALA SEQRES 1 C 12 LYS GLN THR ALA ARG SLL SER THR GLY GLY LYS ALA SEQRES 1 D 12 LYS GLN THR ALA ARG SLL SER THR GLY GLY LYS ALA MODRES 3RIY SLL C 9 LYS MODRES 3RIY SLL D 9 LYS HET SLL C 9 16 HET SLL D 9 16 HET ZN A1001 1 HET NAD A2001 44 HET ZN B1002 1 HET NAD B2002 44 HETNAM SLL (2S)-2-AZANYL-6-[(4-HYDROXY-4-OXO-BUTANOYL) HETNAM 2 SLL AMINO]HEXANOIC ACID HETNAM ZN ZINC ION HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETSYN SLL 6-N-SUCCINYL-L-LYSINE FORMUL 3 SLL 2(C10 H18 N2 O5) FORMUL 5 ZN 2(ZN 2+) FORMUL 6 NAD 2(C21 H27 N7 O14 P2) FORMUL 9 HOH *690(H2 O) HELIX 1 1 SER A 39 ALA A 50 1 12 HELIX 2 2 ALA A 59 GLY A 66 5 8 HELIX 3 3 GLY A 72 GLY A 74 5 3 HELIX 4 4 ALA A 82 ALA A 86 1 5 HELIX 5 5 THR A 87 ASN A 94 1 8 HELIX 6 6 ASN A 94 GLY A 110 1 17 HELIX 7 7 ASN A 115 LYS A 130 1 16 HELIX 8 8 GLU A 144 GLY A 150 1 7 HELIX 9 9 CYS A 181 SER A 185 5 5 HELIX 10 10 PRO A 200 LEU A 204 5 5 HELIX 11 11 GLU A 208 CYS A 212 5 5 HELIX 12 12 ASP A 228 CYS A 242 1 15 HELIX 13 13 PRO A 256 ALA A 258 5 3 HELIX 14 14 MET A 259 ARG A 267 1 9 HELIX 15 15 ALA A 281 PHE A 285 5 5 HELIX 16 16 PRO A 292 ALA A 302 1 11 HELIX 17 17 SER B 39 ALA B 50 1 12 HELIX 18 18 ALA B 59 GLY B 66 5 8 HELIX 19 19 GLY B 72 GLY B 74 5 3 HELIX 20 20 ALA B 82 ALA B 86 1 5 HELIX 21 21 THR B 87 ASN B 94 1 8 HELIX 22 22 ASN B 94 SER B 111 1 18 HELIX 23 23 ASN B 115 LYS B 130 1 16 HELIX 24 24 GLU B 144 GLY B 150 1 7 HELIX 25 25 CYS B 181 SER B 185 5 5 HELIX 26 26 PRO B 200 LEU B 204 5 5 HELIX 27 27 ASP B 228 CYS B 242 1 15 HELIX 28 28 PRO B 256 ALA B 258 5 3 HELIX 29 29 MET B 259 ARG B 267 1 9 HELIX 30 30 ALA B 281 PHE B 285 5 5 HELIX 31 31 PRO B 292 ALA B 302 1 11 SHEET 1 A 6 LEU A 154 GLU A 156 0 SHEET 2 A 6 ARG A 134 THR A 139 1 N VAL A 137 O LEU A 155 SHEET 3 A 6 HIS A 52 SER A 57 1 N ILE A 55 O VAL A 136 SHEET 4 A 6 LEU A 244 VAL A 248 1 O VAL A 248 N ILE A 56 SHEET 5 A 6 VAL A 271 ASN A 275 1 O ALA A 272 N VAL A 247 SHEET 6 A 6 PHE A 287 GLN A 290 1 O PHE A 289 N GLU A 273 SHEET 1 B 2 TYR A 76 TRP A 77 0 SHEET 2 B 2 TRP A 80 GLN A 81 -1 O TRP A 80 N TRP A 77 SHEET 1 C 3 VAL A 172 GLU A 174 0 SHEET 2 C 3 GLY A 159 CYS A 166 -1 N THR A 164 O ALA A 173 SHEET 3 C 3 LEU A 216 VAL A 220 -1 O ARG A 217 N ARG A 165 SHEET 1 D 2 VAL A 254 TYR A 255 0 SHEET 2 D 2 SER D 10 THR D 11 -1 O SER D 10 N TYR A 255 SHEET 1 E 6 LEU B 154 GLU B 156 0 SHEET 2 E 6 ARG B 134 THR B 139 1 N VAL B 137 O LEU B 155 SHEET 3 E 6 HIS B 52 SER B 57 1 N ILE B 53 O ARG B 134 SHEET 4 E 6 LEU B 244 VAL B 248 1 O VAL B 248 N ILE B 56 SHEET 5 E 6 VAL B 271 ASN B 275 1 O ALA B 272 N VAL B 247 SHEET 6 E 6 PHE B 287 GLN B 290 1 O PHE B 289 N GLU B 273 SHEET 1 F 2 TYR B 76 TRP B 77 0 SHEET 2 F 2 TRP B 80 GLN B 81 -1 O TRP B 80 N TRP B 77 SHEET 1 G 3 VAL B 172 GLU B 174 0 SHEET 2 G 3 GLY B 159 CYS B 166 -1 N THR B 164 O ALA B 173 SHEET 3 G 3 LEU B 216 VAL B 220 -1 O ARG B 217 N ARG B 165 SHEET 1 H 2 VAL B 254 TYR B 255 0 SHEET 2 H 2 SER C 10 THR C 11 -1 O SER C 10 N TYR B 255 LINK C ARG C 8 N SLL C 9 1555 1555 1.34 LINK C SLL C 9 N SER C 10 1555 1555 1.34 LINK C ARG D 8 N SLL D 9 1555 1555 1.33 LINK C SLL D 9 N SER D 10 1555 1555 1.32 LINK SG CYS A 166 ZN ZN A1001 1555 1555 2.36 LINK SG CYS A 169 ZN ZN A1001 1555 1555 2.32 LINK SG CYS A 207 ZN ZN A1001 1555 1555 2.38 LINK SG CYS A 212 ZN ZN A1001 1555 1555 2.36 LINK SG CYS B 166 ZN ZN B1002 1555 1555 2.36 LINK SG CYS B 169 ZN ZN B1002 1555 1555 2.24 LINK SG CYS B 207 ZN ZN B1002 1555 1555 2.34 LINK SG CYS B 212 ZN ZN B1002 1555 1555 2.31 CISPEP 1 SER A 178 PRO A 179 0 -6.24 CISPEP 2 TYR A 255 PRO A 256 0 3.97 CISPEP 3 SER B 178 PRO B 179 0 -2.74 CISPEP 4 TYR B 255 PRO B 256 0 7.55 SITE 1 AC1 4 CYS A 166 CYS A 169 CYS A 207 CYS A 212 SITE 1 AC2 29 ALA A 59 GLY A 60 GLU A 64 VAL A 67 SITE 2 AC2 29 PRO A 68 THR A 69 PHE A 70 ARG A 71 SITE 3 AC2 29 GLN A 140 ASN A 141 ILE A 142 ASP A 143 SITE 4 AC2 29 GLY A 249 THR A 250 SER A 251 ASN A 275 SITE 5 AC2 29 THR A 276 GLU A 277 PRO A 292 CYS A 293 SITE 6 AC2 29 HOH A 305 HOH A 343 HOH A 360 HOH A 367 SITE 7 AC2 29 HOH A 412 HOH A 450 HOH A 506 SLL D 9 SITE 8 AC2 29 HOH D 19 SITE 1 AC3 4 CYS B 166 CYS B 169 CYS B 207 CYS B 212 SITE 1 AC4 29 ALA B 59 GLY B 60 GLU B 64 VAL B 67 SITE 2 AC4 29 PRO B 68 THR B 69 PHE B 70 ARG B 71 SITE 3 AC4 29 GLN B 140 ASN B 141 ILE B 142 ASP B 143 SITE 4 AC4 29 HIS B 158 GLY B 249 THR B 250 SER B 251 SITE 5 AC4 29 ASN B 275 THR B 276 GLU B 277 PRO B 292 SITE 6 AC4 29 CYS B 293 HOH B 309 HOH B 383 HOH B 385 SITE 7 AC4 29 HOH B 421 HOH B 458 HOH B 486 SLL C 9 SITE 8 AC4 29 HOH C 199 CRYST1 52.691 69.417 156.321 90.00 90.00 90.00 P 21 21 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 0.018979 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014406 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006397 0.00000