HEADER HYDROLASE 19-SEP-13 4C78 TITLE COMPLEX OF HUMAN SIRT3 WITH BROMO-RESVERATROL AND ACS2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 116-399; COMPND 5 EC: 3.5.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ACETYL-COENZYME A SYNTHETASE 2-LIKE, MITOCHONDRIAL; COMPND 9 CHAIN: C; COMPND 10 FRAGMENT: RESIDUES 638-647; COMPND 11 EC: 6.2.1.1; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PVFT3S; 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, SIRTUIN, INHIBITOR, ACTIVATION, RESVERATROL, SIRT1, KEYWDS 2 METABOLIC SENSOR, METABOLISM, AGING EXPDTA X-RAY DIFFRACTION AUTHOR G.T.T.NGUYEN,M.GERTZ,M.WEYAND,C.STEEGBORN REVDAT 4 20-DEC-23 4C78 1 REMARK LINK REVDAT 3 11-DEC-13 4C78 1 JRNL REVDAT 2 27-NOV-13 4C78 1 JRNL REVDAT 1 20-NOV-13 4C78 0 JRNL AUTH G.T.T.NGUYEN,M.GERTZ,C.STEEGBORN JRNL TITL CRYSTAL STRUCTURES OF SIRT3 COMPLEXES WITH JRNL TITL 2 4'-BROMO-RESVERATROL REVEAL BINDING SITES AND INHIBITION JRNL TITL 3 MECHANISM. JRNL REF CHEM.BIOL. V. 20 1375 2013 JRNL REFN ISSN 1074-5521 JRNL PMID 24211137 JRNL DOI 10.1016/J.CHEMBIOL.2013.09.019 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 19507 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1025 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) : 1427 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.3340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2112 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 125 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.07000 REMARK 3 B22 (A**2) : 1.64000 REMARK 3 B33 (A**2) : -1.71000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.184 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.167 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.137 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.553 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2191 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2146 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2977 ; 1.923 ; 2.001 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4925 ; 0.952 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 267 ; 6.768 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;35.802 ;22.447 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 357 ;16.063 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;17.160 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 337 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2422 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 497 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1071 ; 1.016 ; 0.811 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1070 ; 1.014 ; 0.810 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1334 ; 1.729 ; 1.203 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1335 ; 1.729 ; 1.205 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1120 ; 1.221 ; 1.731 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1121 ; 1.220 ; 1.731 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1643 ; 1.918 ; 1.952 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2610 ; 8.066 ; 8.050 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2570 ; 8.015 ; 7.554 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): 1 ;47.891 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 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 122 A 152 REMARK 3 ORIGIN FOR THE GROUP (A): -13.3608 35.9439 -11.3175 REMARK 3 T TENSOR REMARK 3 T11: 0.2384 T22: 0.2404 REMARK 3 T33: 0.2498 T12: -0.0687 REMARK 3 T13: 0.0208 T23: -0.0140 REMARK 3 L TENSOR REMARK 3 L11: 6.1059 L22: 2.9326 REMARK 3 L33: 8.1764 L12: -0.6258 REMARK 3 L13: 0.1628 L23: 2.5813 REMARK 3 S TENSOR REMARK 3 S11: 0.1286 S12: -0.3987 S13: 0.5604 REMARK 3 S21: -0.0808 S22: -0.1106 S23: -0.0968 REMARK 3 S31: -0.8549 S32: -0.0338 S33: -0.0180 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 153 A 189 REMARK 3 ORIGIN FOR THE GROUP (A): -9.2755 16.7542 -39.3275 REMARK 3 T TENSOR REMARK 3 T11: 0.4356 T22: 0.3222 REMARK 3 T33: 0.2247 T12: -0.0082 REMARK 3 T13: -0.0245 T23: -0.0323 REMARK 3 L TENSOR REMARK 3 L11: 2.6329 L22: 2.2252 REMARK 3 L33: 10.9070 L12: 0.0726 REMARK 3 L13: 0.6360 L23: 1.9798 REMARK 3 S TENSOR REMARK 3 S11: -0.1206 S12: 0.2072 S13: 0.0173 REMARK 3 S21: -0.4887 S22: 0.3250 S23: -0.1984 REMARK 3 S31: 0.2931 S32: 0.7321 S33: -0.2044 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 : A 190 A 311 REMARK 3 ORIGIN FOR THE GROUP (A): -12.0646 14.7076 -22.7303 REMARK 3 T TENSOR REMARK 3 T11: 0.3944 T22: 0.3241 REMARK 3 T33: 0.3047 T12: 0.0462 REMARK 3 T13: -0.1139 T23: -0.0340 REMARK 3 L TENSOR REMARK 3 L11: 0.2412 L22: 2.4628 REMARK 3 L33: 4.8175 L12: 0.4181 REMARK 3 L13: -0.0715 L23: 2.2474 REMARK 3 S TENSOR REMARK 3 S11: 0.0433 S12: -0.0194 S13: -0.0987 REMARK 3 S21: 0.1801 S22: 0.2763 S23: -0.2132 REMARK 3 S31: 0.8918 S32: 0.3213 S33: -0.3196 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 : A 312 A 394 REMARK 3 ORIGIN FOR THE GROUP (A): -12.0960 34.7840 -16.5729 REMARK 3 T TENSOR REMARK 3 T11: 0.2341 T22: 0.2283 REMARK 3 T33: 0.2310 T12: -0.0306 REMARK 3 T13: 0.0540 T23: -0.0211 REMARK 3 L TENSOR REMARK 3 L11: 2.4865 L22: 1.7405 REMARK 3 L33: 4.3914 L12: -0.6432 REMARK 3 L13: 0.9070 L23: 0.4339 REMARK 3 S TENSOR REMARK 3 S11: 0.1078 S12: 0.1182 S13: 0.2890 REMARK 3 S21: -0.3094 S22: 0.0280 S23: -0.0794 REMARK 3 S31: -0.5758 S32: 0.2248 S33: -0.1357 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 : C 2 C 9 REMARK 3 ORIGIN FOR THE GROUP (A): -16.3307 24.5024 -36.0324 REMARK 3 T TENSOR REMARK 3 T11: 0.4482 T22: 0.2173 REMARK 3 T33: 0.3254 T12: 0.0328 REMARK 3 T13: -0.0456 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 2.4895 L22: 14.7773 REMARK 3 L33: 20.9928 L12: 1.6376 REMARK 3 L13: -3.9265 L23: -4.9381 REMARK 3 S TENSOR REMARK 3 S11: 0.1851 S12: 0.0195 S13: 0.4910 REMARK 3 S21: -0.2521 S22: 0.4518 S23: 0.3606 REMARK 3 S31: -1.1253 S32: -0.5658 S33: -0.6369 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. REMARK 4 REMARK 4 4C78 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1290058410. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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) : 0.918 REMARK 200 MONOCHROMATOR : SI(111) MONOCHROMATOR REMARK 200 OPTICS : COLLIMATOR 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 : 37699 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 37.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 2.100 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 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) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.990 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4H8D REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 250 MM (NH4)2SO4, 100 MM BISTRIS PH 6, REMARK 280 21% (W/V) PEG 3350, PH 6.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.30000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 79.85000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.30000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 79.85000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.3 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2039 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 116 REMARK 465 SER A 117 REMARK 465 SER A 118 REMARK 465 ASP A 119 REMARK 465 LYS A 120 REMARK 465 GLY A 121 REMARK 465 PRO A 160 REMARK 465 GLY A 161 REMARK 465 SER A 162 REMARK 465 GLY A 163 REMARK 465 LEU A 164 REMARK 465 TYR A 165 REMARK 465 SER A 166 REMARK 465 ASN A 167 REMARK 465 LEU A 168 REMARK 465 GLN A 169 REMARK 465 GLN A 170 REMARK 465 TYR A 171 REMARK 465 ASP A 395 REMARK 465 GLY A 396 REMARK 465 PRO A 397 REMARK 465 ASP A 398 REMARK 465 LYS A 399 REMARK 465 THR C 0 REMARK 465 ARG C 1 REMARK 465 SER C 2 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 OD2 ASP A 218 O HOH A 2042 2.11 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 A 381 CD GLU A 381 OE2 0.087 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 139 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 313 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG A 384 NE - CZ - NH1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ARG A 384 NE - CZ - NH2 ANGL. DEV. = -5.5 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 ALA A 134 9.74 -64.84 REMARK 500 ARG A 135 21.90 44.96 REMARK 500 ASN A 188 97.70 -165.23 REMARK 500 ASN A 203 -71.11 -79.12 REMARK 500 ASP A 290 47.88 -79.05 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 A1396 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 256 SG REMARK 620 2 CYS A 259 SG 111.2 REMARK 620 3 CYS A 280 SG 102.0 106.3 REMARK 620 4 CYS A 283 SG 94.3 126.2 113.8 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 BVB A 1395 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1396 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4C7B RELATED DB: PDB REMARK 900 COMPLEX OF HUMAN SIRT3 WITH BROMO-RESVERATROL AND FLUOR-DE-LYS REMARK 900 PEPTIDE DBREF 4C78 A 116 399 UNP Q9NTG7 SIR3_HUMAN 116 399 DBREF 4C78 C 0 9 UNP Q9NUB1 ACS2L_HUMAN 638 647 SEQRES 1 A 284 GLY SER SER ASP LYS GLY LYS LEU SER LEU GLN ASP VAL SEQRES 2 A 284 ALA GLU LEU ILE ARG ALA ARG ALA CYS GLN ARG VAL VAL SEQRES 3 A 284 VAL MET VAL GLY ALA GLY ILE SER THR PRO SER GLY ILE SEQRES 4 A 284 PRO ASP PHE ARG SER PRO GLY SER GLY LEU TYR SER ASN SEQRES 5 A 284 LEU GLN GLN TYR ASP LEU PRO TYR PRO GLU ALA ILE PHE SEQRES 6 A 284 GLU LEU PRO PHE PHE PHE HIS ASN PRO LYS PRO PHE PHE SEQRES 7 A 284 THR LEU ALA LYS GLU LEU TYR PRO GLY ASN TYR LYS PRO SEQRES 8 A 284 ASN VAL THR HIS TYR PHE LEU ARG LEU LEU HIS ASP LYS SEQRES 9 A 284 GLY LEU LEU LEU ARG LEU TYR THR GLN ASN ILE ASP GLY SEQRES 10 A 284 LEU GLU ARG VAL SER GLY ILE PRO ALA SER LYS LEU VAL SEQRES 11 A 284 GLU ALA HIS GLY THR PHE ALA SER ALA THR CYS THR VAL SEQRES 12 A 284 CYS GLN ARG PRO PHE PRO GLY GLU ASP ILE ARG ALA ASP SEQRES 13 A 284 VAL MET ALA ASP ARG VAL PRO ARG CYS PRO VAL CYS THR SEQRES 14 A 284 GLY VAL VAL LYS PRO ASP ILE VAL PHE PHE GLY GLU PRO SEQRES 15 A 284 LEU PRO GLN ARG PHE LEU LEU HIS VAL VAL ASP PHE PRO SEQRES 16 A 284 MET ALA ASP LEU LEU LEU ILE LEU GLY THR SER LEU GLU SEQRES 17 A 284 VAL GLU PRO PHE ALA SER LEU THR GLU ALA VAL ARG SER SEQRES 18 A 284 SER VAL PRO ARG LEU LEU ILE ASN ARG ASP LEU VAL GLY SEQRES 19 A 284 PRO LEU ALA TRP HIS PRO ARG SER ARG ASP VAL ALA GLN SEQRES 20 A 284 LEU GLY ASP VAL VAL HIS GLY VAL GLU SER LEU VAL GLU SEQRES 21 A 284 LEU LEU GLY TRP THR GLU GLU MET ARG ASP LEU VAL GLN SEQRES 22 A 284 ARG GLU THR GLY LYS LEU ASP GLY PRO ASP LYS SEQRES 1 C 10 THR ARG SER GLY ALY VAL MET ARG ARG LEU MODRES 4C78 ALY C 4 LYS N(6)-ACETYLLYSINE HET ALY C 4 12 HET BVB A1395 17 HET ZN A1396 1 HETNAM ALY N(6)-ACETYLLYSINE HETNAM BVB 5-[(E)-2-(4-BROMOPHENYL)ETHENYL]BENZENE-1,3-DIOL HETNAM ZN ZINC ION FORMUL 2 ALY C8 H16 N2 O3 FORMUL 3 BVB C14 H11 BR O2 FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *125(H2 O) HELIX 1 1 SER A 124 ALA A 134 1 11 HELIX 2 2 ALA A 146 GLY A 153 5 8 HELIX 3 3 TYR A 175 PHE A 180 5 6 HELIX 4 4 GLU A 181 ASN A 188 1 8 HELIX 5 5 PRO A 189 TYR A 200 1 12 HELIX 6 6 ASN A 207 LYS A 219 1 13 HELIX 7 7 GLY A 232 SER A 237 1 6 HELIX 8 8 PRO A 240 SER A 242 5 3 HELIX 9 9 ILE A 268 ALA A 274 1 7 HELIX 10 10 PRO A 299 LEU A 303 5 5 HELIX 11 11 LEU A 304 ALA A 312 1 9 HELIX 12 12 PRO A 326 GLU A 332 1 7 HELIX 13 13 VAL A 348 HIS A 354 1 7 HELIX 14 14 ASP A 365 GLY A 378 1 14 HELIX 15 15 TRP A 379 LYS A 393 1 15 SHEET 1 AA 6 LEU A 244 GLU A 246 0 SHEET 2 AA 6 LEU A 222 THR A 227 1 O LEU A 225 N VAL A 245 SHEET 3 AA 6 VAL A 140 VAL A 144 1 O VAL A 140 N LEU A 223 SHEET 4 AA 6 LEU A 314 LEU A 318 1 O LEU A 314 N VAL A 141 SHEET 5 AA 6 ARG A 340 ASN A 344 1 O LEU A 341 N ILE A 317 SHEET 6 AA 6 ASP A 359 LEU A 363 1 O VAL A 360 N LEU A 342 SHEET 1 AB 3 PRO A 262 PRO A 264 0 SHEET 2 AB 3 GLY A 249 CYS A 256 -1 O ALA A 254 N PHE A 263 SHEET 3 AB 3 VAL A 287 ILE A 291 -1 O LYS A 288 N THR A 255 LINK C GLY C 3 N ALY C 4 1555 1555 1.34 LINK C ALY C 4 N VAL C 5 1555 1555 1.32 LINK SG CYS A 256 ZN ZN A1396 1555 1555 2.29 LINK SG CYS A 259 ZN ZN A1396 1555 1555 2.32 LINK SG CYS A 280 ZN ZN A1396 1555 1555 2.34 LINK SG CYS A 283 ZN ZN A1396 1555 1555 2.29 CISPEP 1 GLU A 325 PRO A 326 0 1.53 SITE 1 AC1 8 ARG A 139 MET A 311 ASP A 313 ARG A 335 SITE 2 AC1 8 GLU A 371 GLU A 381 ARG A 384 HOH A2122 SITE 1 AC2 4 CYS A 256 CYS A 259 CYS A 280 CYS A 283 CRYST1 34.700 52.600 159.700 90.00 90.00 90.00 P 2 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.028818 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019011 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006262 0.00000