HEADER HYDROLASE 21-JUL-14 4UTN TITLE CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH SUCCINYLATED TITLE 2 CPS1-PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC CORE, RESIDUES 30-298; COMPND 5 SYNONYM: REGULATORY PROTEIN SIR2 HOMOLOG 5, SIRTUIN 5; COMPND 6 EC: 3.5.1.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SUCCINYL-CPS1-PEPTIDE; COMPND 10 CHAIN: D; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: CODONPLUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET151; 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, REGULATORY ENZYME, ROSSMANN-FOLD, ZINC-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.PANNEK,M.GERTZ,C.STEEGBORN REVDAT 3 10-JAN-24 4UTN 1 REMARK LINK REVDAT 2 08-OCT-14 4UTN 1 JRNL REVDAT 1 20-AUG-14 4UTN 0 JRNL AUTH C.ROESSLER,T.NOWAK,M.PANNEK,M.GERTZ,G.T.NGUYEN,M.SCHARFE, JRNL AUTH 2 I.BORN,W.SIPPL,C.STEEGBORN,M.SCHUTKOWSKI JRNL TITL CHEMICAL PROBING OF THE HUMAN SIRTUIN 5 ACTIVE SITE REVEALS JRNL TITL 2 ITS SUBSTRATE ACYL SPECIFICITY AND PEPTIDE-BASED INHIBITORS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 53 10728 2014 JRNL REFN ISSN 1433-7851 JRNL PMID 25111069 JRNL DOI 10.1002/ANIE.201402679 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 75.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 14400 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) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 758 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1012 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.3010 REMARK 3 BIN FREE R VALUE SET COUNT : 53 REMARK 3 BIN FREE R VALUE : 0.3520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4162 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 17 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.71000 REMARK 3 B22 (A**2) : 0.71000 REMARK 3 B33 (A**2) : -2.29000 REMARK 3 B12 (A**2) : 0.35000 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): 0.440 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.381 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 43.640 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.924 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4310 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4076 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5838 ; 1.673 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9399 ; 1.151 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 533 ; 6.624 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 186 ;36.961 ;22.742 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 690 ;16.090 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;18.357 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 627 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4829 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 987 ; 0.003 ; 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): 2138 ; 2.251 ; 4.389 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2137 ; 2.251 ; 4.387 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2666 ; 3.730 ; 6.577 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2171 ; 2.567 ; 4.650 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 : 2 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 35 A 298 REMARK 3 ORIGIN FOR THE GROUP (A): 22.5846 26.3920 -6.3676 REMARK 3 T TENSOR REMARK 3 T11: 0.0786 T22: 0.1668 REMARK 3 T33: 0.0877 T12: 0.0342 REMARK 3 T13: -0.0190 T23: 0.0595 REMARK 3 L TENSOR REMARK 3 L11: 3.2240 L22: 1.7938 REMARK 3 L33: 1.8371 L12: 0.6278 REMARK 3 L13: -0.4137 L23: -0.5821 REMARK 3 S TENSOR REMARK 3 S11: -0.0577 S12: 0.2213 S13: -0.2452 REMARK 3 S21: -0.0112 S22: -0.0090 S23: -0.0104 REMARK 3 S31: 0.1864 S32: 0.1784 S33: 0.0667 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 : B 33 B 298 REMARK 3 ORIGIN FOR THE GROUP (A): -3.0609 29.7145 -27.3837 REMARK 3 T TENSOR REMARK 3 T11: 0.1198 T22: 0.1645 REMARK 3 T33: 0.0915 T12: 0.0154 REMARK 3 T13: -0.0621 T23: 0.0704 REMARK 3 L TENSOR REMARK 3 L11: 3.1141 L22: 1.4534 REMARK 3 L33: 4.8664 L12: -0.1211 REMARK 3 L13: 1.3167 L23: -0.9658 REMARK 3 S TENSOR REMARK 3 S11: -0.0250 S12: -0.2830 S13: -0.1877 REMARK 3 S21: 0.0534 S22: 0.2325 S23: 0.1906 REMARK 3 S31: 0.0821 S32: -0.5493 S33: -0.2075 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. U VALUES WITH TLS ADDED. STRUCTURE REFINED USING REMARK 3 PROSMART WITH PDB-ID 3RIY R.A. NICHOLLS, F. LONG AND G.N. REMARK 3 MURSHUDOV (2012) LOW RESOLUTION REFINEMENT TOOLS IN REFMAC5. REMARK 3 ACTA CRYST. D. REMARK 4 REMARK 4 4UTN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1290061283. 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 : 7.4 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) : 0.9184 REMARK 200 MONOCHROMATOR : SI111 CRYSTAL REMARK 200 OPTICS : MIRROR 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 : 15155 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.18000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 8.50 REMARK 200 R MERGE FOR SHELL (I) : 1.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 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 2NYR REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.1 M HEPES PH 7.4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 209.94667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 104.97333 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 157.46000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 52.48667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 262.43333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 209.94667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 104.97333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 52.48667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 157.46000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 262.43333 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: 990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 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: 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 24 REMARK 465 ILE A 25 REMARK 465 ASP A 26 REMARK 465 PRO A 27 REMARK 465 PHE A 28 REMARK 465 THR A 29 REMARK 465 THR A 30 REMARK 465 ARG A 31 REMARK 465 PRO A 32 REMARK 465 SER A 33 REMARK 465 SER A 34 REMARK 465 GLN A 279 REMARK 465 ARG A 280 REMARK 465 PHE A 281 REMARK 465 GLY B 24 REMARK 465 ILE B 25 REMARK 465 ASP B 26 REMARK 465 PRO B 27 REMARK 465 PHE B 28 REMARK 465 THR B 29 REMARK 465 THR B 30 REMARK 465 ARG B 31 REMARK 465 PRO B 32 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 74 -135.28 47.54 REMARK 500 ASP A 90 70.27 -154.32 REMARK 500 CYS A 208 -67.92 -90.17 REMARK 500 THR A 246 -175.70 -173.20 REMARK 500 PRO A 276 -159.20 -67.21 REMARK 500 PHE B 66 15.10 80.68 REMARK 500 ARG B 74 -136.27 48.67 REMARK 500 ASP B 90 70.41 -156.25 REMARK 500 SER B 164 -61.27 -93.97 REMARK 500 ILE B 195 99.99 40.24 REMARK 500 CYS B 208 -66.30 -102.57 REMARK 500 THR B 246 -175.37 -173.75 REMARK 500 PHE B 281 -152.78 -80.51 REMARK 500 SLL D 4 119.17 -35.92 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 A1300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 162 SG REMARK 620 2 CYS A 165 SG 105.2 REMARK 620 3 CYS A 203 SG 110.5 114.8 REMARK 620 4 CYS A 208 SG 104.3 118.0 103.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 162 SG REMARK 620 2 CYS B 165 SG 108.7 REMARK 620 3 CYS B 203 SG 108.0 119.4 REMARK 620 4 CYS B 208 SG 94.2 117.1 106.3 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 EPE B 1299 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS B 1301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UTR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH REMARK 900 GLUTARYLATED CPS1-PEPTIDE REMARK 900 RELATED ID: 4UTV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH 3-PHENYL- REMARK 900 SUCCINYLATED CPS1-PEPTIDE REMARK 900 RELATED ID: 4UTX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH 3-NITRO- REMARK 900 PROPIONYLATED CPS1-PEPTIDE REMARK 900 RELATED ID: 4UTZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH REMARK 900 ADIPOYLATED CPS1-PEPTIDE REMARK 900 RELATED ID: 4UU7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH 3-METHYL- REMARK 900 SUCCINYLATED CPS1-PEPTIDE REMARK 900 RELATED ID: 4UU8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH 3,3- REMARK 900 DIMETHYL-SUCCINYLATED CPS1-PEPTIDE REMARK 900 RELATED ID: 4UUA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH 3S-Z-AMINO- REMARK 900 SUCCINYLATED CPS1-PEPTIDE REMARK 900 RELATED ID: 4UUB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ZEBRAFISH SIRTUIN 5 IN COMPLEX WITH 2R-BUTYL- REMARK 900 SUCCINYLATED CPS1-PEPTIDE REMARK 999 REMARK 999 SEQUENCE REMARK 999 BENZOYLATED GLYCINE AT POSITION 1 SUCCINYLATED LYSINE AT REMARK 999 POSITION 4 DBREF 4UTN A 30 298 UNP Q6DHI5 SIR5_DANRE 30 298 DBREF 4UTN B 30 298 UNP Q6DHI5 SIR5_DANRE 30 298 DBREF 4UTN D 1 8 PDB 4UTN 4UTN 1 8 SEQADV 4UTN GLY A 24 UNP Q6DHI5 EXPRESSION TAG SEQADV 4UTN ILE A 25 UNP Q6DHI5 EXPRESSION TAG SEQADV 4UTN ASP A 26 UNP Q6DHI5 EXPRESSION TAG SEQADV 4UTN PRO A 27 UNP Q6DHI5 EXPRESSION TAG SEQADV 4UTN PHE A 28 UNP Q6DHI5 EXPRESSION TAG SEQADV 4UTN THR A 29 UNP Q6DHI5 EXPRESSION TAG SEQADV 4UTN GLY B 24 UNP Q6DHI5 EXPRESSION TAG SEQADV 4UTN ILE B 25 UNP Q6DHI5 EXPRESSION TAG SEQADV 4UTN ASP B 26 UNP Q6DHI5 EXPRESSION TAG SEQADV 4UTN PRO B 27 UNP Q6DHI5 EXPRESSION TAG SEQADV 4UTN PHE B 28 UNP Q6DHI5 EXPRESSION TAG SEQADV 4UTN THR B 29 UNP Q6DHI5 EXPRESSION TAG SEQRES 1 A 275 GLY ILE ASP PRO PHE THR THR ARG PRO SER SER ASP LEU SEQRES 2 A 275 THR ALA PHE ARG GLU HIS PHE ALA LYS ALA LYS HIS ILE SEQRES 3 A 275 ALA ILE ILE THR GLY ALA GLY VAL SER ALA GLU SER GLY SEQRES 4 A 275 VAL PRO THR PHE ARG GLY PRO GLY GLY PHE TRP ARG LYS SEQRES 5 A 275 TRP GLN ALA GLN ASP LEU ALA THR PRO GLU ALA PHE SER SEQRES 6 A 275 ARG ASP PRO SER LEU VAL TRP GLU PHE TYR HIS TYR ARG SEQRES 7 A 275 ARG GLU VAL MET ARG SER LYS MET PRO ASN PRO ALA HIS SEQRES 8 A 275 LEU ALA ILE ALA GLU CYS GLU ALA ARG LEU GLY GLN GLN SEQRES 9 A 275 GLY ARG SER VAL VAL ILE ILE THR GLN ASN ILE ASP GLU SEQRES 10 A 275 LEU HIS HIS ARG ALA GLY SER LYS HIS VAL TYR GLU ILE SEQRES 11 A 275 HIS GLY SER LEU PHE LYS THR ARG CYS MET SER CYS GLY SEQRES 12 A 275 GLU VAL LYS ALA ASN HIS LYS SER PRO ILE CYS PRO ALA SEQRES 13 A 275 LEU ASP GLY LYS GLY ALA PRO ASP PRO ASN THR LYS GLU SEQRES 14 A 275 ALA ARG ILE PRO VAL GLU LEU LEU PRO ARG CYS GLU ARG SEQRES 15 A 275 LYS SER CYS ASN GLY LEU LEU ARG PRO HIS VAL VAL TRP SEQRES 16 A 275 PHE GLY GLU THR LEU ASP SER ASP ILE LEU THR ALA VAL SEQRES 17 A 275 GLU ARG GLU LEU GLU LYS CYS ASP LEU CYS LEU VAL VAL SEQRES 18 A 275 GLY THR SER SER ILE VAL TYR PRO ALA ALA MET PHE ALA SEQRES 19 A 275 PRO GLN VAL ALA SER ARG GLY VAL PRO VAL ALA GLU PHE SEQRES 20 A 275 ASN MET GLU CYS THR PRO ALA THR GLN ARG PHE LYS TYR SEQRES 21 A 275 HIS PHE GLU GLY PRO CYS GLY SER THR LEU PRO PRO ALA SEQRES 22 A 275 LEU GLU SEQRES 1 B 275 GLY ILE ASP PRO PHE THR THR ARG PRO SER SER ASP LEU SEQRES 2 B 275 THR ALA PHE ARG GLU HIS PHE ALA LYS ALA LYS HIS ILE SEQRES 3 B 275 ALA ILE ILE THR GLY ALA GLY VAL SER ALA GLU SER GLY SEQRES 4 B 275 VAL PRO THR PHE ARG GLY PRO GLY GLY PHE TRP ARG LYS SEQRES 5 B 275 TRP GLN ALA GLN ASP LEU ALA THR PRO GLU ALA PHE SER SEQRES 6 B 275 ARG ASP PRO SER LEU VAL TRP GLU PHE TYR HIS TYR ARG SEQRES 7 B 275 ARG GLU VAL MET ARG SER LYS MET PRO ASN PRO ALA HIS SEQRES 8 B 275 LEU ALA ILE ALA GLU CYS GLU ALA ARG LEU GLY GLN GLN SEQRES 9 B 275 GLY ARG SER VAL VAL ILE ILE THR GLN ASN ILE ASP GLU SEQRES 10 B 275 LEU HIS HIS ARG ALA GLY SER LYS HIS VAL TYR GLU ILE SEQRES 11 B 275 HIS GLY SER LEU PHE LYS THR ARG CYS MET SER CYS GLY SEQRES 12 B 275 GLU VAL LYS ALA ASN HIS LYS SER PRO ILE CYS PRO ALA SEQRES 13 B 275 LEU ASP GLY LYS GLY ALA PRO ASP PRO ASN THR LYS GLU SEQRES 14 B 275 ALA ARG ILE PRO VAL GLU LEU LEU PRO ARG CYS GLU ARG SEQRES 15 B 275 LYS SER CYS ASN GLY LEU LEU ARG PRO HIS VAL VAL TRP SEQRES 16 B 275 PHE GLY GLU THR LEU ASP SER ASP ILE LEU THR ALA VAL SEQRES 17 B 275 GLU ARG GLU LEU GLU LYS CYS ASP LEU CYS LEU VAL VAL SEQRES 18 B 275 GLY THR SER SER ILE VAL TYR PRO ALA ALA MET PHE ALA SEQRES 19 B 275 PRO GLN VAL ALA SER ARG GLY VAL PRO VAL ALA GLU PHE SEQRES 20 B 275 ASN MET GLU CYS THR PRO ALA THR GLN ARG PHE LYS TYR SEQRES 21 B 275 HIS PHE GLU GLY PRO CYS GLY SER THR LEU PRO PRO ALA SEQRES 22 B 275 LEU GLU SEQRES 1 D 9 BEZ GLY VAL LEU SLL GLU TYR GLY VAL MODRES 4UTN SLL D 4 LYS HET BEZ D 0 8 HET SLL D 4 16 HET ZN A1300 1 HET EPE B1299 15 HET ZN B1300 1 HET DMS B1301 4 HET EDO B1302 4 HETNAM BEZ BENZOIC ACID HETNAM SLL (2S)-2-AZANYL-6-[(4-HYDROXY-4-OXO-BUTANOYL) HETNAM 2 SLL AMINO]HEXANOIC ACID HETNAM ZN ZINC ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM DMS DIMETHYL SULFOXIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN SLL 6-N-SUCCINYL-L-LYSINE HETSYN EPE HEPES HETSYN EDO ETHYLENE GLYCOL FORMUL 3 BEZ C7 H6 O2 FORMUL 3 SLL C10 H18 N2 O5 FORMUL 4 ZN 2(ZN 2+) FORMUL 5 EPE C8 H18 N2 O4 S FORMUL 7 DMS C2 H6 O S FORMUL 8 EDO C2 H6 O2 FORMUL 9 HOH *17(H2 O) HELIX 1 1 ASP A 35 ALA A 46 1 12 HELIX 2 2 ALA A 55 GLU A 60 1 6 HELIX 3 3 GLN A 77 ALA A 82 1 6 HELIX 4 4 THR A 83 ASP A 90 1 8 HELIX 5 5 ASP A 90 ARG A 106 1 17 HELIX 6 6 ASN A 111 GLN A 127 1 17 HELIX 7 7 GLU A 140 GLY A 146 1 7 HELIX 8 8 CYS A 177 ASP A 181 5 5 HELIX 9 9 PRO A 196 LEU A 200 5 5 HELIX 10 10 ASP A 224 CYS A 238 1 15 HELIX 11 11 PRO A 252 ARG A 263 1 12 HELIX 12 12 PRO A 288 GLU A 298 1 11 HELIX 13 13 ASP B 35 ALA B 46 1 12 HELIX 14 14 ALA B 55 GLU B 60 1 6 HELIX 15 15 GLN B 77 ALA B 82 1 6 HELIX 16 16 THR B 83 ASP B 90 1 8 HELIX 17 17 ASP B 90 ARG B 106 1 17 HELIX 18 18 ASN B 111 GLN B 126 1 16 HELIX 19 19 GLU B 140 GLY B 146 1 7 HELIX 20 20 CYS B 177 ASP B 181 5 5 HELIX 21 21 PRO B 196 LEU B 200 5 5 HELIX 22 22 ASP B 224 CYS B 238 1 15 HELIX 23 23 PRO B 252 MET B 255 5 4 HELIX 24 24 PHE B 256 ARG B 263 1 8 HELIX 25 25 PRO B 276 ARG B 280 5 5 HELIX 26 26 PRO B 288 GLU B 298 1 11 HELIX 27 27 SLL D 4 VAL D 8 5 5 SHEET 1 AA 6 VAL A 150 GLU A 152 0 SHEET 2 AA 6 SER A 130 THR A 135 1 O ILE A 133 N TYR A 151 SHEET 3 AA 6 HIS A 48 THR A 53 1 O ILE A 49 N VAL A 132 SHEET 4 AA 6 LEU A 240 VAL A 244 1 O LEU A 240 N ALA A 50 SHEET 5 AA 6 VAL A 267 ASN A 271 1 O ALA A 268 N VAL A 243 SHEET 6 AA 6 TYR A 283 GLU A 286 1 O TYR A 283 N GLU A 269 SHEET 1 AB 3 VAL A 168 ALA A 170 0 SHEET 2 AB 3 GLY A 155 CYS A 162 -1 O THR A 160 N LYS A 169 SHEET 3 AB 3 LEU A 212 VAL A 216 -1 O ARG A 213 N ARG A 161 SHEET 1 BA 6 VAL B 150 GLU B 152 0 SHEET 2 BA 6 SER B 130 THR B 135 1 O ILE B 133 N TYR B 151 SHEET 3 BA 6 HIS B 48 THR B 53 1 O ILE B 49 N VAL B 132 SHEET 4 BA 6 LEU B 240 VAL B 244 1 O LEU B 240 N ALA B 50 SHEET 5 BA 6 VAL B 267 ASN B 271 1 O ALA B 268 N VAL B 243 SHEET 6 BA 6 TYR B 283 GLU B 286 1 O TYR B 283 N GLU B 269 SHEET 1 BB 3 VAL B 168 ALA B 170 0 SHEET 2 BB 3 GLY B 155 CYS B 162 -1 O THR B 160 N LYS B 169 SHEET 3 BB 3 LEU B 212 VAL B 216 -1 O ARG B 213 N ARG B 161 SSBOND 1 CYS A 274 CYS B 274 1555 12554 2.03 LINK C BEZ D 0 N GLY D 1 1555 1555 1.36 LINK C LEU D 3 N SLL D 4 1555 1555 1.33 LINK C SLL D 4 N GLU D 5 1555 1555 1.33 LINK SG CYS A 162 ZN ZN A1300 1555 1555 2.30 LINK SG CYS A 165 ZN ZN A1300 1555 1555 2.35 LINK SG CYS A 203 ZN ZN A1300 1555 1555 2.31 LINK SG CYS A 208 ZN ZN A1300 1555 1555 2.34 LINK SG CYS B 162 ZN ZN B1300 1555 1555 2.35 LINK SG CYS B 165 ZN ZN B1300 1555 1555 2.33 LINK SG CYS B 203 ZN ZN B1300 1555 1555 2.35 LINK SG CYS B 208 ZN ZN B1300 1555 1555 2.30 CISPEP 1 SER A 174 PRO A 175 0 -4.79 CISPEP 2 TYR A 251 PRO A 252 0 -0.08 CISPEP 3 SER B 174 PRO B 175 0 -4.57 CISPEP 4 TYR B 251 PRO B 252 0 4.45 SITE 1 AC1 11 THR A 229 GLU A 232 THR B 65 ALA B 78 SITE 2 AC1 11 ALA B 82 ARG B 101 HIS B 154 VAL B 217 SITE 3 AC1 11 PHE B 219 GLU B 221 EDO B1302 SITE 1 AC2 4 CYS B 162 CYS B 165 CYS B 203 CYS B 208 SITE 1 AC3 4 CYS A 162 CYS A 165 CYS A 203 CYS A 208 SITE 1 AC4 4 ARG A 144 ALA A 145 ARG B 144 ALA B 145 SITE 1 AC5 4 GLN B 136 ASN B 137 ILE B 138 EPE B1299 CRYST1 87.440 87.440 314.920 90.00 90.00 120.00 P 65 2 2 24 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 0.011436 0.006603 0.000000 0.00000 SCALE2 0.000000 0.013206 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003175 0.00000 MTRIX1 1 -0.748260 -0.550700 -0.369910 25.69092 1 MTRIX2 1 -0.533610 0.168310 0.828820 42.56148 1 MTRIX3 1 -0.394160 0.817560 -0.419800 -42.38670 1