PDB Short entry for 3RIG HEADER HYDROLASE 13-APR-11 3RIG 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 THIOACETYL-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: THIS HUMAN HISTONE 3 N-TERMINAL WAS CHEMICALLY SOURCE 14 MODIFIED ON RESIDUE LYSINE 9 WITH THIOACETYL. KEYWDS PROTEIN LYSINE DEMALONYLASE/DESUCCINYLASE, ZN-BINDING DOMAIN, KEYWDS 2 ROSSMANN FOLD, MITOCHONDRIA, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHOU REVDAT 4 01-NOV-23 3RIG 1 REMARK SEQADV LINK REVDAT 3 08-NOV-17 3RIG 1 REMARK REVDAT 2 11-APR-12 3RIG 1 JRNL REVDAT 1 23-NOV-11 3RIG 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 38693 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1950 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2682 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 147 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4084 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 176 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.20000 REMARK 3 B22 (A**2) : -0.47000 REMARK 3 B33 (A**2) : 0.28000 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): 0.179 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.148 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.826 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4270 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5799 ; 1.856 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 542 ; 6.929 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 186 ;34.577 ;22.473 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 678 ;16.801 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;19.197 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 631 ; 0.127 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3279 ; 0.010 ; 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): 2666 ; 1.058 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4293 ; 1.796 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1604 ; 2.737 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1497 ; 4.282 ; 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 : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 36 A 274 REMARK 3 ORIGIN FOR THE GROUP (A): 10.1350 -9.3150 -18.2270 REMARK 3 T TENSOR REMARK 3 T11: 0.0082 T22: 0.2730 REMARK 3 T33: 0.0434 T12: 0.0063 REMARK 3 T13: -0.0035 T23: -0.0166 REMARK 3 L TENSOR REMARK 3 L11: 3.5055 L22: 1.0507 REMARK 3 L33: 2.8600 L12: -0.4718 REMARK 3 L13: -2.5735 L23: 0.3005 REMARK 3 S TENSOR REMARK 3 S11: 0.1354 S12: 0.2946 S13: 0.1220 REMARK 3 S21: -0.0540 S22: 0.0030 S23: 0.0177 REMARK 3 S31: -0.0760 S32: -0.2637 S33: -0.1383 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 275 A 302 REMARK 3 ORIGIN FOR THE GROUP (A): 21.2950 3.9370 -28.2870 REMARK 3 T TENSOR REMARK 3 T11: 0.4052 T22: 0.2633 REMARK 3 T33: 0.2845 T12: 0.0639 REMARK 3 T13: 0.2600 T23: 0.0513 REMARK 3 L TENSOR REMARK 3 L11: 3.7573 L22: 2.8005 REMARK 3 L33: 9.1412 L12: 0.7791 REMARK 3 L13: -0.9960 L23: 2.8928 REMARK 3 S TENSOR REMARK 3 S11: 0.6945 S12: 0.1206 S13: 0.8612 REMARK 3 S21: -0.5444 S22: -0.0294 S23: -0.0306 REMARK 3 S31: -1.6740 S32: -0.4300 S33: -0.6651 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 : B 36 B 59 REMARK 3 ORIGIN FOR THE GROUP (A): 3.2520 -7.0980 -47.5710 REMARK 3 T TENSOR REMARK 3 T11: 0.0716 T22: 1.6214 REMARK 3 T33: 0.2577 T12: 0.1405 REMARK 3 T13: -0.0124 T23: 0.3193 REMARK 3 L TENSOR REMARK 3 L11: 3.6545 L22: 4.1790 REMARK 3 L33: 8.1595 L12: -1.2983 REMARK 3 L13: 0.8161 L23: -1.4229 REMARK 3 S TENSOR REMARK 3 S11: -0.2762 S12: -0.5617 S13: -0.0850 REMARK 3 S21: 0.1016 S22: 0.6370 S23: 0.2858 REMARK 3 S31: -0.0580 S32: -2.3699 S33: -0.3609 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 74 B 229 REMARK 3 ORIGIN FOR THE GROUP (A): 26.7230 -7.1250 -62.8570 REMARK 3 T TENSOR REMARK 3 T11: 0.0263 T22: 0.2432 REMARK 3 T33: 0.0943 T12: 0.0096 REMARK 3 T13: -0.0355 T23: 0.0051 REMARK 3 L TENSOR REMARK 3 L11: 2.0764 L22: 0.8775 REMARK 3 L33: 4.5792 L12: 0.4650 REMARK 3 L13: -0.0174 L23: -1.3962 REMARK 3 S TENSOR REMARK 3 S11: 0.0174 S12: -0.0933 S13: -0.1259 REMARK 3 S21: -0.1010 S22: 0.0289 S23: 0.0174 REMARK 3 S31: 0.2421 S32: 0.1575 S33: -0.0463 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 230 B 302 REMARK 3 ORIGIN FOR THE GROUP (A): 4.8460 -4.8370 -55.8590 REMARK 3 T TENSOR REMARK 3 T11: 0.0671 T22: 1.1113 REMARK 3 T33: 0.2508 T12: 0.1154 REMARK 3 T13: -0.0126 T23: 0.2260 REMARK 3 L TENSOR REMARK 3 L11: 1.6776 L22: 0.4630 REMARK 3 L33: 8.1244 L12: -0.4310 REMARK 3 L13: 1.6688 L23: -1.6907 REMARK 3 S TENSOR REMARK 3 S11: -0.1359 S12: -0.4957 S13: -0.1409 REMARK 3 S21: 0.1041 S22: 0.6051 S23: 0.2247 REMARK 3 S31: -0.4692 S32: -2.2907 S33: -0.4693 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 3RIG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-APR-11. REMARK 100 THE DEPOSITION ID IS D_1000064970. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.917 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, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41492 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.34600 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 2B4Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 0.1M CHES, PH 9.5, 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 26.26900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.37450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.93800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 78.37450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.26900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.93800 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 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: 1000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 GLY A 30 REMARK 465 SER A 62 REMARK 465 ALA A 63 REMARK 465 GLU A 64 REMARK 465 SER A 65 REMARK 465 GLY A 66 REMARK 465 VAL A 67 REMARK 465 PRO A 68 REMARK 465 THR A 69 REMARK 465 PHE A 70 REMARK 465 ARG A 71 REMARK 465 GLY A 72 REMARK 465 ALA A 73 REMARK 465 GLY B 30 REMARK 465 SER B 31 REMARK 465 GLY B 60 REMARK 465 VAL B 61 REMARK 465 SER B 62 REMARK 465 ALA B 63 REMARK 465 GLU B 64 REMARK 465 SER B 65 REMARK 465 GLY B 66 REMARK 465 VAL B 67 REMARK 465 PRO B 68 REMARK 465 THR B 69 REMARK 465 PHE B 70 REMARK 465 ARG B 71 REMARK 465 GLY B 72 REMARK 465 LYS C 4 REMARK 465 GLN C 5 REMARK 465 GLY C 12 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 GLY D 12 REMARK 465 GLY D 13 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 OE2 GLU B 273 OG1 THR B 282 1.93 REMARK 500 OD2 ASP B 236 O HOH B 337 2.17 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 CYS A 207 CA - CB - SG ANGL. DEV. = 8.9 DEGREES REMARK 500 THR A 250 N - CA - C ANGL. DEV. = -25.3 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 THR A 33 84.32 -61.53 REMARK 500 ARG A 78 -136.56 58.02 REMARK 500 ASN A 94 68.39 -160.32 REMARK 500 SER A 168 -62.45 -98.18 REMARK 500 CYS A 212 -80.14 -105.04 REMARK 500 SER A 251 -19.43 109.08 REMARK 500 THR B 33 86.78 94.11 REMARK 500 ARG B 78 -132.16 56.03 REMARK 500 ASN B 94 71.06 -151.49 REMARK 500 SER B 251 132.65 176.48 REMARK 500 VAL B 253 92.85 43.88 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 GLY A 249 THR A 250 -70.43 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 106.4 REMARK 620 3 CYS A 207 SG 109.9 109.7 REMARK 620 4 CYS A 212 SG 113.1 114.0 103.8 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 98.9 REMARK 620 3 CYS B 207 SG 108.2 102.6 REMARK 620 4 CYS B 212 SG 113.9 117.0 114.5 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 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NHE 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 NHE B 2002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RIY RELATED DB: PDB DBREF 3RIG A 34 302 UNP Q9NXA8 SIRT5_HUMAN 34 302 DBREF 3RIG B 34 302 UNP Q9NXA8 SIRT5_HUMAN 34 302 DBREF 3RIG C 4 15 PDB 3RIG 3RIG 4 15 DBREF 3RIG D 4 15 PDB 3RIG 3RIG 4 15 SEQADV 3RIG GLY A 30 UNP Q9NXA8 EXPRESSION TAG SEQADV 3RIG SER A 31 UNP Q9NXA8 EXPRESSION TAG SEQADV 3RIG PHE A 32 UNP Q9NXA8 EXPRESSION TAG SEQADV 3RIG THR A 33 UNP Q9NXA8 EXPRESSION TAG SEQADV 3RIG GLY B 30 UNP Q9NXA8 EXPRESSION TAG SEQADV 3RIG SER B 31 UNP Q9NXA8 EXPRESSION TAG SEQADV 3RIG PHE B 32 UNP Q9NXA8 EXPRESSION TAG SEQADV 3RIG 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 TLY SER THR GLY GLY LYS ALA SEQRES 1 D 12 LYS GLN THR ALA ARG TLY SER THR GLY GLY LYS ALA MODRES 3RIG TLY C 9 LYS MODRES 3RIG TLY D 9 LYS HET TLY C 9 12 HET TLY D 9 12 HET ZN A1001 1 HET NHE A2001 13 HET ZN B1002 1 HET NHE B2002 13 HETNAM TLY (2S)-2-AZANYL-6-(ETHANETHIOYLAMINO)HEXANOIC ACID HETNAM ZN ZINC ION HETNAM NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID HETSYN TLY 6-N-THIOLACETYL-L-LYSINE HETSYN NHE N-CYCLOHEXYLTAURINE; CHES FORMUL 3 TLY 2(C8 H16 N2 O2 S) FORMUL 5 ZN 2(ZN 2+) FORMUL 6 NHE 2(C8 H17 N O3 S) FORMUL 9 HOH *176(H2 O) HELIX 1 1 SER A 39 ALA A 50 1 12 HELIX 2 2 GLN A 83 LEU A 85 5 3 HELIX 3 3 THR A 87 ASN A 94 1 8 HELIX 4 4 ASN A 94 LYS A 112 1 19 HELIX 5 5 ASN A 115 GLN A 131 1 17 HELIX 6 6 GLU A 144 GLY A 150 1 7 HELIX 7 7 CYS A 181 SER A 185 5 5 HELIX 8 8 PRO A 200 LEU A 204 5 5 HELIX 9 9 ASP A 228 CYS A 242 1 15 HELIX 10 10 PRO A 256 ALA A 258 5 3 HELIX 11 11 MET A 259 ARG A 267 1 9 HELIX 12 12 ALA A 281 PHE A 285 5 5 HELIX 13 13 PRO A 292 LEU A 301 1 10 HELIX 14 14 SER B 39 ALA B 50 1 12 HELIX 15 15 ALA B 82 ALA B 86 1 5 HELIX 16 16 THR B 87 ASN B 94 1 8 HELIX 17 17 ASN B 94 SER B 111 1 18 HELIX 18 18 ASN B 115 GLN B 131 1 17 HELIX 19 19 GLU B 144 ALA B 149 1 6 HELIX 20 20 CYS B 181 SER B 185 5 5 HELIX 21 21 PRO B 200 LEU B 204 5 5 HELIX 22 22 ASP B 228 CYS B 242 1 15 HELIX 23 23 PRO B 256 ALA B 258 5 3 HELIX 24 24 MET B 259 ARG B 267 1 9 HELIX 25 25 ALA B 281 PHE B 285 5 5 HELIX 26 26 PRO B 292 LEU B 301 1 10 SHEET 1 A 6 LEU A 154 GLU A 156 0 SHEET 2 A 6 ARG A 134 THR A 139 1 N THR A 139 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 PHE A 274 1 O PHE A 274 N VAL A 247 SHEET 6 A 6 PHE A 287 PHE A 289 1 O PHE A 287 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 HIS A 219 N SER A 160 SHEET 1 D 6 LEU B 154 GLU B 156 0 SHEET 2 D 6 ARG B 134 THR B 139 1 N THR B 139 O LEU B 155 SHEET 3 D 6 HIS B 52 SER B 57 1 N ILE B 55 O ILE B 138 SHEET 4 D 6 LEU B 244 VAL B 248 1 O VAL B 248 N ILE B 56 SHEET 5 D 6 VAL B 271 ASN B 275 1 O PHE B 274 N VAL B 247 SHEET 6 D 6 PHE B 287 GLN B 290 1 O PHE B 287 N VAL B 271 SHEET 1 E 2 TYR B 76 TRP B 77 0 SHEET 2 E 2 TRP B 80 GLN B 81 -1 O TRP B 80 N TRP B 77 SHEET 1 F 3 VAL B 172 GLU B 174 0 SHEET 2 F 3 GLY B 159 CYS B 166 -1 N THR B 164 O ALA B 173 SHEET 3 F 3 LEU B 216 VAL B 220 -1 O ARG B 217 N ARG B 165 LINK C ARG C 8 N TLY C 9 1555 1555 1.32 LINK C TLY C 9 N SER C 10 1555 1555 1.32 LINK C ARG D 8 N TLY D 9 1555 1555 1.34 LINK C TLY D 9 N SER D 10 1555 1555 1.34 LINK SG CYS A 166 ZN ZN A1001 1555 1555 2.19 LINK SG CYS A 169 ZN ZN A1001 1555 1555 2.66 LINK SG CYS A 207 ZN ZN A1001 1555 1555 1.93 LINK SG CYS A 212 ZN ZN A1001 1555 1555 2.41 LINK SG CYS B 166 ZN ZN B1002 1555 1555 2.38 LINK SG CYS B 169 ZN ZN B1002 1555 1555 2.15 LINK SG CYS B 207 ZN ZN B1002 1555 1555 2.31 LINK SG CYS B 212 ZN ZN B1002 1555 1555 2.37 CISPEP 1 SER A 178 PRO A 179 0 -10.53 CISPEP 2 THR A 250 SER A 251 0 5.20 CISPEP 3 TYR A 255 PRO A 256 0 -0.25 CISPEP 4 SER B 178 PRO B 179 0 -1.03 CISPEP 5 SER B 251 SER B 252 0 16.95 CISPEP 6 TYR B 255 PRO B 256 0 -1.47 SITE 1 AC1 4 CYS A 166 CYS A 169 CYS A 207 CYS A 212 SITE 1 AC2 9 GLY A 74 PHE A 101 TYR A 102 ARG A 105 SITE 2 AC2 9 ILE A 142 VAL A 254 HOH A 337 HOH A 358 SITE 3 AC2 9 TLY C 9 SITE 1 AC3 4 CYS B 166 CYS B 169 CYS B 207 CYS B 212 SITE 1 AC4 9 ALA B 82 GLN B 83 PHE B 101 TYR B 102 SITE 2 AC4 9 ARG B 105 ILE B 142 VAL B 254 HOH B 367 SITE 3 AC4 9 TLY D 9 CRYST1 52.538 67.876 156.749 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 0.019034 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014733 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006380 0.00000