PDB Short entry for 4F4U HEADER HYDROLASE 11-MAY-12 4F4U TITLE THE BICYCLIC INTERMEDIATE STRUCTURE PROVIDES INSIGHTS INTO THE TITLE 2 DESUCCINYLATION MECHANISM OF SIRT5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT LYSINE DEMALONYLASE AND DESUCCINYLASE COMPND 3 SIRTUIN-5, MITOCHONDRIAL; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: UNP RESIDUE 34-302; COMPND 6 SYNONYM: SIR2-LIKE PROTEIN 5; COMPND 7 EC: 3.5.1.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: PEPTIDE FROM HISTONE H3.1; COMPND 11 CHAIN: C, D; COMPND 12 FRAGMENT: UNP RESIDUE 5-16; COMPND 13 SYNONYM: HISTONE H3/A, HISTONE H3/B, HISTONE H3/C, HISTONE H3/D, COMPND 14 HISTONE H3/F, HISTONE H3/H, HISTONE H3/I, HISTONE H3/J, HISTONE H3/K, COMPND 15 HISTONE H3/L; COMPND 16 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 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS ZN-BINDING DOMAIN, ROSSMANN FOLD DOMAIN, NAD-DEPENDENT DEMALONYLASE KEYWDS 2 AND DESUCCINYLASE, MITOCHONDRIAL SIRTUIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHOU,Q.HAO REVDAT 4 08-NOV-23 4F4U 1 REMARK SEQADV LINK REVDAT 3 15-NOV-17 4F4U 1 REMARK REVDAT 2 19-SEP-12 4F4U 1 JRNL REVDAT 1 20-JUN-12 4F4U 0 JRNL AUTH Y.ZHOU,H.ZHANG,B.HE,J.DU,H.LIN,R.A.CERIONE,Q.HAO JRNL TITL THE BICYCLIC INTERMEDIATE STRUCTURE PROVIDES INSIGHTS INTO JRNL TITL 2 THE DESUCCINYLATION MECHANISM OF HUMAN SIRTUIN 5 (SIRT5) JRNL REF J.BIOL.CHEM. V. 287 28307 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22767592 JRNL DOI 10.1074/JBC.M112.384511 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1051 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 38428 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1927 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 4286 REMARK 3 ANGLE : 0.995 5804 REMARK 3 CHIRALITY : 0.064 630 REMARK 3 PLANARITY : 0.005 766 REMARK 3 DIHEDRAL : 13.226 1576 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 33:68) REMARK 3 ORIGIN FOR THE GROUP (A): -21.1156 -4.1844 29.7185 REMARK 3 T TENSOR REMARK 3 T11: 0.6066 T22: 1.0853 REMARK 3 T33: 0.3739 T12: 0.2898 REMARK 3 T13: 0.0016 T23: 0.1090 REMARK 3 L TENSOR REMARK 3 L11: 3.3357 L22: 3.4534 REMARK 3 L33: 2.5839 L12: -1.1720 REMARK 3 L13: 1.0112 L23: -0.6506 REMARK 3 S TENSOR REMARK 3 S11: -0.2588 S12: -0.6511 S13: 0.1222 REMARK 3 S21: 0.3065 S22: 0.2792 S23: 0.3708 REMARK 3 S31: -0.7415 S32: -1.2498 S33: -0.0091 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 69:109) REMARK 3 ORIGIN FOR THE GROUP (A): 3.1050 1.1297 10.5372 REMARK 3 T TENSOR REMARK 3 T11: 0.3791 T22: 0.2659 REMARK 3 T33: 0.2870 T12: 0.0729 REMARK 3 T13: -0.0304 T23: 0.0057 REMARK 3 L TENSOR REMARK 3 L11: 3.9434 L22: 7.3916 REMARK 3 L33: 7.6660 L12: 1.3143 REMARK 3 L13: 3.5155 L23: -1.1552 REMARK 3 S TENSOR REMARK 3 S11: -0.3054 S12: -0.1348 S13: 0.3590 REMARK 3 S21: -0.3176 S22: 0.0602 S23: 0.3594 REMARK 3 S31: -0.2582 S32: -0.4421 S33: 0.3348 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 110:156) REMARK 3 ORIGIN FOR THE GROUP (A): -9.6898 -12.5854 28.5859 REMARK 3 T TENSOR REMARK 3 T11: 0.5343 T22: 0.5123 REMARK 3 T33: 0.3112 T12: 0.1490 REMARK 3 T13: 0.0272 T23: 0.0841 REMARK 3 L TENSOR REMARK 3 L11: 2.2609 L22: 3.6060 REMARK 3 L33: 7.5581 L12: 1.7686 REMARK 3 L13: -0.9102 L23: -1.6261 REMARK 3 S TENSOR REMARK 3 S11: -0.2183 S12: -0.3727 S13: -0.1314 REMARK 3 S21: 0.0599 S22: 0.2079 S23: -0.0863 REMARK 3 S31: 0.7326 S32: -0.3105 S33: 0.0956 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 157:242) REMARK 3 ORIGIN FOR THE GROUP (A): 1.6875 -10.3585 10.5575 REMARK 3 T TENSOR REMARK 3 T11: 0.6302 T22: 0.3020 REMARK 3 T33: 0.3276 T12: 0.0516 REMARK 3 T13: 0.0520 T23: 0.0317 REMARK 3 L TENSOR REMARK 3 L11: 4.8059 L22: 1.4905 REMARK 3 L33: 2.3781 L12: 1.7370 REMARK 3 L13: -0.8419 L23: -1.0767 REMARK 3 S TENSOR REMARK 3 S11: -0.4899 S12: 0.0541 S13: -0.5985 REMARK 3 S21: -0.5516 S22: 0.1916 S23: -0.2094 REMARK 3 S31: 0.7557 S32: -0.0458 S33: 0.2851 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 243:302) REMARK 3 ORIGIN FOR THE GROUP (A): -21.4909 -1.7772 23.7537 REMARK 3 T TENSOR REMARK 3 T11: 0.7099 T22: 1.0247 REMARK 3 T33: 0.5387 T12: 0.2740 REMARK 3 T13: -0.1016 T23: 0.1592 REMARK 3 L TENSOR REMARK 3 L11: 0.8060 L22: 0.6496 REMARK 3 L33: 4.1102 L12: -0.1859 REMARK 3 L13: -0.1256 L23: 0.7652 REMARK 3 S TENSOR REMARK 3 S11: -0.3328 S12: -0.2547 S13: 0.4229 REMARK 3 S21: 0.0366 S22: 0.6153 S23: 0.4441 REMARK 3 S31: -1.1149 S32: -1.5876 S33: -0.2363 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B AND RESID 32:63) REMARK 3 ORIGIN FOR THE GROUP (A): 0.5055 -0.7824 49.0103 REMARK 3 T TENSOR REMARK 3 T11: 0.7288 T22: 0.4309 REMARK 3 T33: 0.4954 T12: -0.1149 REMARK 3 T13: 0.1855 T23: 0.0033 REMARK 3 L TENSOR REMARK 3 L11: 1.4276 L22: 4.3059 REMARK 3 L33: 3.2235 L12: 1.5890 REMARK 3 L13: -0.6437 L23: 0.6270 REMARK 3 S TENSOR REMARK 3 S11: 0.2287 S12: 0.1050 S13: 0.6891 REMARK 3 S21: -0.6792 S22: 0.2014 S23: -0.5665 REMARK 3 S31: -1.1407 S32: 0.4033 S33: -0.3532 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN B AND RESID 75:108) REMARK 3 ORIGIN FOR THE GROUP (A): -28.6720 -4.0848 67.8021 REMARK 3 T TENSOR REMARK 3 T11: 0.4809 T22: 0.3719 REMARK 3 T33: 0.4444 T12: -0.1225 REMARK 3 T13: 0.1357 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 8.0672 L22: 2.7357 REMARK 3 L33: 8.1993 L12: -2.3067 REMARK 3 L13: 1.7430 L23: 0.7852 REMARK 3 S TENSOR REMARK 3 S11: -0.3156 S12: 0.7866 S13: 0.6024 REMARK 3 S21: 0.0788 S22: 0.3007 S23: -0.0335 REMARK 3 S31: -0.7842 S32: 0.1635 S33: 0.0724 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN B AND RESID 109:157) REMARK 3 ORIGIN FOR THE GROUP (A): -11.1992 -12.6507 50.0499 REMARK 3 T TENSOR REMARK 3 T11: 0.4089 T22: 0.4547 REMARK 3 T33: 0.2511 T12: 0.0266 REMARK 3 T13: -0.0026 T23: -0.0535 REMARK 3 L TENSOR REMARK 3 L11: 3.7023 L22: 5.8261 REMARK 3 L33: 6.4512 L12: -1.2006 REMARK 3 L13: -1.1358 L23: 0.7963 REMARK 3 S TENSOR REMARK 3 S11: 0.3111 S12: 0.6530 S13: -0.1427 REMARK 3 S21: -0.6806 S22: -0.4180 S23: 0.1001 REMARK 3 S31: 0.0842 S32: -1.1170 S33: 0.0709 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN B AND RESID 158:227) REMARK 3 ORIGIN FOR THE GROUP (A): -28.5688 -14.3778 68.2624 REMARK 3 T TENSOR REMARK 3 T11: 0.3900 T22: 0.4333 REMARK 3 T33: 0.5115 T12: -0.1313 REMARK 3 T13: 0.1421 T23: -0.1360 REMARK 3 L TENSOR REMARK 3 L11: 5.2933 L22: 2.4083 REMARK 3 L33: 2.4506 L12: -0.6561 REMARK 3 L13: -0.5012 L23: -0.0314 REMARK 3 S TENSOR REMARK 3 S11: -0.1660 S12: 0.6834 S13: -0.9150 REMARK 3 S21: 0.3698 S22: 0.1196 S23: 0.3763 REMARK 3 S31: -0.0224 S32: -0.0653 S33: 0.0279 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN B AND RESID 228:302) REMARK 3 ORIGIN FOR THE GROUP (A): -2.8976 -1.9829 56.5399 REMARK 3 T TENSOR REMARK 3 T11: 0.5060 T22: 0.3164 REMARK 3 T33: 0.3847 T12: -0.0719 REMARK 3 T13: 0.0820 T23: -0.0261 REMARK 3 L TENSOR REMARK 3 L11: 2.7781 L22: 5.2085 REMARK 3 L33: 5.3578 L12: 0.3906 REMARK 3 L13: -1.6559 L23: 1.7298 REMARK 3 S TENSOR REMARK 3 S11: 0.3981 S12: 0.0366 S13: 0.3682 REMARK 3 S21: -0.4246 S22: -0.1169 S23: -0.4722 REMARK 3 S31: -1.1977 S32: 0.2000 S33: -0.2710 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4F4U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072456. 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 : 8.5 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) : 0.918 REMARK 200 MONOCHROMATOR : HORIZONTAL BENT SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38953 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.48800 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 3RIY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 4000, 6% GLYCEROL, PH 8.5, REMARK 280 VAPOR 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 26.34350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.81350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.51250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 78.81350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.34350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.51250 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, 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: 1190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 31 REMARK 465 PHE A 32 REMARK 465 ARG A 71 REMARK 465 GLY A 72 REMARK 465 ALA A 73 REMARK 465 GLY A 74 REMARK 465 GLY B 30 REMARK 465 SER B 31 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 ALA B 73 REMARK 465 GLY B 74 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 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 A 273 OG1 THR A 279 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 O GLY A 211 ND2 ASN A 226 4545 2.19 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 ALA A 34 149.90 -171.15 REMARK 500 ARG A 78 -126.40 52.09 REMARK 500 ASN A 94 69.43 -155.62 REMARK 500 SER A 168 -62.46 -101.11 REMARK 500 ARG B 78 -132.86 56.14 REMARK 500 ASN B 94 68.70 -151.99 REMARK 500 SER B 168 -68.45 -104.10 REMARK 500 ALA B 210 106.67 -50.86 REMARK 500 CYS B 212 -76.17 -94.66 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 62.9 REMARK 620 3 CYS A 207 SG 110.3 120.0 REMARK 620 4 CYS A 212 SG 104.3 104.7 132.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 166 SG REMARK 620 2 CYS B 169 SG 103.6 REMARK 620 3 CYS B 207 SG 103.9 96.3 REMARK 620 4 CYS B 212 SG 104.5 125.8 120.0 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 ZN B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4F56 RELATED DB: PDB DBREF 4F4U A 34 302 UNP Q9NXA8 SIRT5_HUMAN 34 302 DBREF 4F4U B 34 302 UNP Q9NXA8 SIRT5_HUMAN 34 302 DBREF 4F4U C 4 15 UNP P68431 H31_HUMAN 5 16 DBREF 4F4U D 4 15 UNP P68431 H31_HUMAN 5 16 SEQADV 4F4U GLY A 30 UNP Q9NXA8 EXPRESSION TAG SEQADV 4F4U SER A 31 UNP Q9NXA8 EXPRESSION TAG SEQADV 4F4U PHE A 32 UNP Q9NXA8 EXPRESSION TAG SEQADV 4F4U THR A 33 UNP Q9NXA8 EXPRESSION TAG SEQADV 4F4U GLY B 30 UNP Q9NXA8 EXPRESSION TAG SEQADV 4F4U SER B 31 UNP Q9NXA8 EXPRESSION TAG SEQADV 4F4U PHE B 32 UNP Q9NXA8 EXPRESSION TAG SEQADV 4F4U 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 4F4U SLL C 9 LYS MODRES 4F4U SLL D 9 LYS HET SLL C 9 16 HET SLL D 9 16 HET ZN A1001 1 HET ZN B 401 1 HETNAM SLL (2S)-2-AZANYL-6-[(4-HYDROXY-4-OXO-BUTANOYL) HETNAM 2 SLL AMINO]HEXANOIC ACID HETNAM ZN ZINC ION HETSYN SLL 6-N-SUCCINYL-L-LYSINE FORMUL 3 SLL 2(C10 H18 N2 O5) FORMUL 5 ZN 2(ZN 2+) FORMUL 7 HOH *238(H2 O) HELIX 1 1 SER A 39 ALA A 50 1 12 HELIX 2 2 ALA A 59 GLU A 64 1 6 HELIX 3 3 GLN A 81 ALA A 86 1 6 HELIX 4 4 THR A 87 ASN A 94 1 8 HELIX 5 5 ASN A 94 SER A 111 1 18 HELIX 6 6 ASN A 115 LYS A 130 1 16 HELIX 7 7 GLU A 144 GLY A 150 1 7 HELIX 8 8 CYS A 181 SER A 185 5 5 HELIX 9 9 PRO A 200 LEU A 204 5 5 HELIX 10 10 ASP A 228 ALA A 240 1 13 HELIX 11 11 PRO A 256 ALA A 258 5 3 HELIX 12 12 MET A 259 ALA A 266 1 8 HELIX 13 13 ALA A 281 PHE A 285 5 5 HELIX 14 14 PRO A 292 LEU A 301 1 10 HELIX 15 15 SER B 39 ALA B 50 1 12 HELIX 16 16 ALA B 59 ALA B 63 5 5 HELIX 17 17 ALA B 82 ALA B 86 1 5 HELIX 18 18 THR B 87 ASN B 94 1 8 HELIX 19 19 ASN B 94 SER B 111 1 18 HELIX 20 20 ASN B 115 LYS B 130 1 16 HELIX 21 21 GLU B 144 GLY B 150 1 7 HELIX 22 22 CYS B 181 SER B 185 5 5 HELIX 23 23 PRO B 200 LEU B 204 5 5 HELIX 24 24 ASP B 228 CYS B 242 1 15 HELIX 25 25 PRO B 256 ALA B 258 5 3 HELIX 26 26 MET B 259 ALA B 266 1 8 HELIX 27 27 ALA B 281 PHE B 285 5 5 HELIX 28 28 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 VAL A 137 O LEU A 155 SHEET 3 A 6 HIS A 52 SER A 57 1 N ILE A 53 O ARG A 134 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 3 VAL A 172 GLU A 174 0 SHEET 2 B 3 GLY A 159 CYS A 166 -1 N THR A 164 O ALA A 173 SHEET 3 B 3 LEU A 216 VAL A 220 -1 O ARG A 217 N ARG A 165 SHEET 1 C 6 LEU B 154 GLU B 156 0 SHEET 2 C 6 ARG B 134 THR B 139 1 N VAL B 137 O LEU B 155 SHEET 3 C 6 HIS B 52 SER B 57 1 N ILE B 55 O VAL B 136 SHEET 4 C 6 LEU B 244 VAL B 248 1 O VAL B 248 N ILE B 56 SHEET 5 C 6 VAL B 271 ASN B 275 1 O ALA B 272 N CYS B 245 SHEET 6 C 6 PHE B 287 GLN B 290 1 O PHE B 289 N GLU B 273 SHEET 1 D 2 TYR B 76 TRP B 77 0 SHEET 2 D 2 TRP B 80 GLN B 81 -1 O TRP B 80 N TRP B 77 SHEET 1 E 3 VAL B 172 GLU B 174 0 SHEET 2 E 3 GLY B 159 CYS B 166 -1 N THR B 164 O ALA B 173 SHEET 3 E 3 LEU B 216 VAL B 220 -1 O ARG B 217 N ARG B 165 SHEET 1 F 2 VAL B 254 TYR B 255 0 SHEET 2 F 2 SER D 10 THR D 11 -1 O SER D 10 N TYR B 255 LINK C ARG C 8 N SLL C 9 1555 1555 1.35 LINK C SLL C 9 N SER C 10 1555 1555 1.32 LINK C ARG D 8 N SLL D 9 1555 1555 1.32 LINK C SLL D 9 N SER D 10 1555 1555 1.32 LINK SG CYS A 166 ZN ZN A1001 1555 1555 2.47 LINK SG CYS A 169 ZN ZN A1001 1555 1555 2.13 LINK SG CYS A 207 ZN ZN A1001 1555 1555 2.36 LINK SG CYS A 212 ZN ZN A1001 1555 1555 2.30 LINK SG CYS B 166 ZN ZN B 401 1555 1555 2.33 LINK SG CYS B 169 ZN ZN B 401 1555 1555 2.17 LINK SG CYS B 207 ZN ZN B 401 1555 1555 2.29 LINK SG CYS B 212 ZN ZN B 401 1555 1555 2.29 CISPEP 1 SER A 178 PRO A 179 0 -0.85 CISPEP 2 TYR A 255 PRO A 256 0 -2.61 CISPEP 3 SER B 178 PRO B 179 0 0.84 CISPEP 4 TYR B 255 PRO B 256 0 0.57 SITE 1 AC1 4 CYS A 166 CYS A 169 CYS A 207 CYS A 212 SITE 1 AC2 4 CYS B 166 CYS B 169 CYS B 207 CYS B 212 CRYST1 52.687 67.025 157.627 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 0.018980 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014920 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006344 0.00000