HEADER HYDROLASE 31-OCT-16 5H4D TITLE CRYSTAL STRUCTURE OF HSIRT3 IN COMPLEX WITH A SPECIFIC AGONIST TITLE 2 AMIODARONE HYDROCHLORIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL; COMPND 3 CHAIN: A, H; COMPND 4 FRAGMENT: UNP RESIDUES 121-391; COMPND 5 SYNONYM: HSIRT3,REGULATORY PROTEIN SIR2 HOMOLOG 3,SIR2-LIKE PROTEIN COMPND 6 3; COMPND 7 EC: 3.5.1.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: ARG-HIS-LYS; COMPND 11 CHAIN: D, C; 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 GENE: SIRT3, SIR2L3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SIRT3 AMIODARONE AGONIST, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.ZHANG,L.FU,J.LIU,B.LIU REVDAT 3 05-APR-23 5H4D 1 COMPND SOURCE REMARK DBREF REVDAT 3 2 1 SEQRES HET HETNAM HETSYN REVDAT 3 3 1 FORMUL SHEET LINK SITE REVDAT 3 4 1 ATOM REVDAT 2 22-NOV-17 5H4D 1 REMARK REVDAT 1 08-NOV-17 5H4D 0 JRNL AUTH S.ZHANG,L.FU,J.LIU,B.LIU JRNL TITL CRYSTAL STRUCTURE OF HSIRT3 IN COMPLEX WITH A SPECIFIC JRNL TITL 2 AGONIST AMIODARONE HYDROCHLORIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.21 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 77.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 59.2 REMARK 3 NUMBER OF REFLECTIONS : 5583 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) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.372 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 285 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) : 3.21 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.29 REMARK 3 REFLECTION IN BIN (WORKING SET) : 429 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 61.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE SET COUNT : 22 REMARK 3 BIN FREE R VALUE : 0.4940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4332 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 194 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.89000 REMARK 3 B22 (A**2) : 0.89000 REMARK 3 B33 (A**2) : -2.88000 REMARK 3 B12 (A**2) : 0.44000 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): 1.299 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.813 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 47.808 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.904 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.613 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4645 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4452 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6329 ; 1.309 ; 2.032 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10234 ; 0.905 ; 3.008 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 544 ; 6.855 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 195 ;35.576 ;22.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 715 ;16.744 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;14.629 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 698 ; 0.060 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5089 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1059 ; 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): 2196 ; 1.461 ; 3.464 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2196 ; 1.460 ; 3.464 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2732 ; 2.607 ; 5.195 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5H4D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1300001420. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 197 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5871 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 77.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 59.5 REMARK 200 DATA REDUNDANCY : 1.200 REMARK 200 R MERGE (I) : 0.17400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 65.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.10 REMARK 200 R MERGE FOR SHELL (I) : 0.74300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES SODIUM PH 7.5, 10%(V/V) 2 REMARK 280 -PROPANOL, 20%(W/V) POLYETHYLENE GLYCOL 4,000, EVAPORATION, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 57.28000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.07062 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 41.13467 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 57.28000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 33.07062 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 41.13467 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 57.28000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 33.07062 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 41.13467 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.14125 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 82.26933 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 66.14125 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 82.26933 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 66.14125 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 82.26933 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 APPLY THE FOLLOWING TO CHAINS: D, H 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PHE H 157 CG CD1 CD2 CE1 CE2 CZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O GLN H 228 O2D NAD H 406 1.95 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 NE ARG D 1 OAO BBI A 403 5555 2.15 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 LYS D 3 CA - C - N ANGL. DEV. = 14.5 DEGREES REMARK 500 LYS D 3 O - C - N ANGL. DEV. = -16.4 DEGREES REMARK 500 LYS C 3 O - C - N ANGL. DEV. = 11.3 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 SER A 124 -156.02 -94.93 REMARK 500 ARG A 135 38.70 74.44 REMARK 500 PHE A 157 -42.11 -26.12 REMARK 500 SER A 159 109.32 -37.29 REMARK 500 PRO A 160 75.43 -66.16 REMARK 500 PRO A 201 111.54 -35.09 REMARK 500 GLU A 246 89.35 -66.61 REMARK 500 PHE A 251 51.40 -93.89 REMARK 500 THR A 257 20.46 -79.06 REMARK 500 VAL A 258 -67.57 -128.24 REMARK 500 VAL A 282 -75.93 -82.76 REMARK 500 ASP A 290 42.71 -88.45 REMARK 500 PHE A 294 109.67 -55.40 REMARK 500 LEU A 314 122.92 -173.09 REMARK 500 PHE A 327 -39.23 -34.95 REMARK 500 PRO A 350 2.03 -69.46 REMARK 500 SER H 124 -148.23 -80.12 REMARK 500 ARG H 135 48.35 -4.51 REMARK 500 PRO H 155 -145.14 -77.84 REMARK 500 ASP H 172 71.20 -55.71 REMARK 500 ALA H 178 -32.26 -38.85 REMARK 500 PHE H 180 35.97 -95.16 REMARK 500 PRO H 183 6.29 -61.95 REMARK 500 ASN H 207 -168.05 -100.97 REMARK 500 ASP H 218 -38.23 -39.69 REMARK 500 SER H 242 -8.23 -57.24 REMARK 500 GLN H 260 18.66 59.81 REMARK 500 ALA H 274 53.45 -108.38 REMARK 500 ASP H 275 74.83 14.82 REMARK 500 LEU H 314 107.85 -164.00 REMARK 500 ALA H 328 -84.34 -65.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LYS D 3 -11.48 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 A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 256 SG REMARK 620 2 CYS A 280 SG 113.6 REMARK 620 3 CYS A 283 SG 102.6 115.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN H 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS H 256 SG REMARK 620 2 CYS H 259 SG 93.2 REMARK 620 3 CYS H 280 SG 112.6 91.3 REMARK 620 4 CYS H 283 SG 112.0 106.4 130.6 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BBI A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG H 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN H 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BBI H 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD H 406 DBREF 5H4D A 121 391 UNP Q9NTG7 SIR3_HUMAN 121 391 DBREF 5H4D D 1 4 PDB 5H4D 5H4D 1 4 DBREF 5H4D H 121 391 UNP Q9NTG7 SIR3_HUMAN 121 391 DBREF 5H4D C 1 4 PDB 5H4D 5H4D 1 4 SEQRES 1 A 271 GLY LYS LEU SER LEU GLN ASP VAL ALA GLU LEU ILE ARG SEQRES 2 A 271 ALA ARG ALA CYS GLN ARG VAL VAL VAL MET VAL GLY ALA SEQRES 3 A 271 GLY ILE SER THR PRO SER GLY ILE PRO ASP PHE ARG SER SEQRES 4 A 271 PRO GLY SER GLY LEU TYR SER ASN LEU GLN GLN TYR ASP SEQRES 5 A 271 LEU PRO TYR PRO GLU ALA ILE PHE GLU LEU PRO PHE PHE SEQRES 6 A 271 PHE HIS ASN PRO LYS PRO PHE PHE THR LEU ALA LYS GLU SEQRES 7 A 271 LEU TYR PRO GLY ASN TYR LYS PRO ASN VAL THR HIS TYR SEQRES 8 A 271 PHE LEU ARG LEU LEU HIS ASP LYS GLY LEU LEU LEU ARG SEQRES 9 A 271 LEU TYR THR GLN ASN ILE ASP GLY LEU GLU ARG VAL SER SEQRES 10 A 271 GLY ILE PRO ALA SER LYS LEU VAL GLU ALA HIS GLY THR SEQRES 11 A 271 PHE ALA SER ALA THR CYS THR VAL CYS GLN ARG PRO PHE SEQRES 12 A 271 PRO GLY GLU ASP ILE ARG ALA ASP VAL MET ALA ASP ARG SEQRES 13 A 271 VAL PRO ARG CYS PRO VAL CYS THR GLY VAL VAL LYS PRO SEQRES 14 A 271 ASP ILE VAL PHE PHE GLY GLU PRO LEU PRO GLN ARG PHE SEQRES 15 A 271 LEU LEU HIS VAL VAL ASP PHE PRO MET ALA ASP LEU LEU SEQRES 16 A 271 LEU ILE LEU GLY THR SER LEU GLU VAL GLU PRO PHE ALA SEQRES 17 A 271 SER LEU THR GLU ALA VAL ARG SER SER VAL PRO ARG LEU SEQRES 18 A 271 LEU ILE ASN ARG ASP LEU VAL GLY PRO LEU ALA TRP HIS SEQRES 19 A 271 PRO ARG SER ARG ASP VAL ALA GLN LEU GLY ASP VAL VAL SEQRES 20 A 271 HIS GLY VAL GLU SER LEU VAL GLU LEU LEU GLY TRP THR SEQRES 21 A 271 GLU GLU MET ARG ASP LEU VAL GLN ARG GLU THR SEQRES 1 D 4 ARG HIS LYS ALY SEQRES 1 H 271 GLY LYS LEU SER LEU GLN ASP VAL ALA GLU LEU ILE ARG SEQRES 2 H 271 ALA ARG ALA CYS GLN ARG VAL VAL VAL MET VAL GLY ALA SEQRES 3 H 271 GLY ILE SER THR PRO SER GLY ILE PRO ASP PHE ARG SER SEQRES 4 H 271 PRO GLY SER GLY LEU TYR SER ASN LEU GLN GLN TYR ASP SEQRES 5 H 271 LEU PRO TYR PRO GLU ALA ILE PHE GLU LEU PRO PHE PHE SEQRES 6 H 271 PHE HIS ASN PRO LYS PRO PHE PHE THR LEU ALA LYS GLU SEQRES 7 H 271 LEU TYR PRO GLY ASN TYR LYS PRO ASN VAL THR HIS TYR SEQRES 8 H 271 PHE LEU ARG LEU LEU HIS ASP LYS GLY LEU LEU LEU ARG SEQRES 9 H 271 LEU TYR THR GLN ASN ILE ASP GLY LEU GLU ARG VAL SER SEQRES 10 H 271 GLY ILE PRO ALA SER LYS LEU VAL GLU ALA HIS GLY THR SEQRES 11 H 271 PHE ALA SER ALA THR CYS THR VAL CYS GLN ARG PRO PHE SEQRES 12 H 271 PRO GLY GLU ASP ILE ARG ALA ASP VAL MET ALA ASP ARG SEQRES 13 H 271 VAL PRO ARG CYS PRO VAL CYS THR GLY VAL VAL LYS PRO SEQRES 14 H 271 ASP ILE VAL PHE PHE GLY GLU PRO LEU PRO GLN ARG PHE SEQRES 15 H 271 LEU LEU HIS VAL VAL ASP PHE PRO MET ALA ASP LEU LEU SEQRES 16 H 271 LEU ILE LEU GLY THR SER LEU GLU VAL GLU PRO PHE ALA SEQRES 17 H 271 SER LEU THR GLU ALA VAL ARG SER SER VAL PRO ARG LEU SEQRES 18 H 271 LEU ILE ASN ARG ASP LEU VAL GLY PRO LEU ALA TRP HIS SEQRES 19 H 271 PRO ARG SER ARG ASP VAL ALA GLN LEU GLY ASP VAL VAL SEQRES 20 H 271 HIS GLY VAL GLU SER LEU VAL GLU LEU LEU GLY TRP THR SEQRES 21 H 271 GLU GLU MET ARG ASP LEU VAL GLN ARG GLU THR SEQRES 1 C 4 ARG HIS LYS ALY HET ALY D 4 12 HET ALY C 4 12 HET ZN A 401 1 HET MG A 402 1 HET BBI A 403 31 HET NAD A 404 44 HET MCM D 101 13 HET PEG H 401 7 HET ZN H 402 1 HET PEG H 403 7 HET MG H 404 1 HET BBI H 405 31 HET NAD H 406 44 HET MCM C 101 13 HETNAM ALY N(6)-ACETYLLYSINE HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM BBI (2-BUTYL-1-BENZOFURAN-3-YL){4-[2-(DIETHYLAMINO)ETHOXY]- HETNAM 2 BBI 3,5-DIIODOPHENYL}METHANONE HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM MCM 7-AMINO-4-METHYL-CHROMEN-2-ONE HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN MCM 7-AMINO-4-METHYLCOUMARIN FORMUL 2 ALY 2(C8 H16 N2 O3) FORMUL 5 ZN 2(ZN 2+) FORMUL 6 MG 2(MG 2+) FORMUL 7 BBI 2(C25 H29 I2 N O3) FORMUL 8 NAD 2(C21 H27 N7 O14 P2) FORMUL 9 MCM 2(C10 H9 N O2) FORMUL 10 PEG 2(C4 H10 O3) HELIX 1 AA1 LEU A 125 ALA A 134 1 10 HELIX 2 AA2 ALA A 146 GLY A 153 5 8 HELIX 3 AA3 LEU A 164 GLN A 170 1 7 HELIX 4 AA4 TYR A 175 PHE A 180 5 6 HELIX 5 AA5 GLU A 181 ASN A 188 1 8 HELIX 6 AA6 PRO A 189 TYR A 200 1 12 HELIX 7 AA7 ASN A 207 LYS A 219 1 13 HELIX 8 AA8 GLY A 232 SER A 237 1 6 HELIX 9 AA9 GLU A 266 MET A 273 1 8 HELIX 10 AB1 PRO A 299 LEU A 303 5 5 HELIX 11 AB2 LEU A 304 PHE A 309 1 6 HELIX 12 AB3 ALA A 328 GLU A 332 5 5 HELIX 13 AB4 VAL A 348 ALA A 352 5 5 HELIX 14 AB5 ASP A 365 GLY A 378 1 14 HELIX 15 AB6 TRP A 379 THR A 391 1 13 HELIX 16 AB7 LEU H 125 ALA H 134 1 10 HELIX 17 AB8 SER H 162 TYR H 171 1 10 HELIX 18 AB9 TYR H 175 PHE H 180 5 6 HELIX 19 AC1 GLU H 181 PHE H 186 1 6 HELIX 20 AC2 PRO H 189 TYR H 200 1 12 HELIX 21 AC3 ASN H 207 LYS H 219 1 13 HELIX 22 AC4 GLY H 232 SER H 237 1 6 HELIX 23 AC5 PRO H 240 SER H 242 5 3 HELIX 24 AC6 ILE H 268 ALA H 274 1 7 HELIX 25 AC7 PRO H 299 LEU H 303 5 5 HELIX 26 AC8 LEU H 304 PHE H 309 1 6 HELIX 27 AC9 SER H 329 VAL H 334 1 6 HELIX 28 AD1 GLY H 349 HIS H 354 1 6 HELIX 29 AD2 VAL H 366 GLY H 378 1 13 HELIX 30 AD3 TRP H 379 GLU H 390 1 12 SHEET 1 AA1 6 LEU A 244 GLU A 246 0 SHEET 2 AA1 6 LEU A 222 THR A 227 1 N LEU A 225 O VAL A 245 SHEET 3 AA1 6 VAL A 140 VAL A 144 1 N VAL A 142 O ARG A 224 SHEET 4 AA1 6 LEU A 315 LEU A 318 1 O LEU A 316 N MET A 143 SHEET 5 AA1 6 ARG A 340 ASN A 344 1 O LEU A 341 N LEU A 315 SHEET 6 AA1 6 ASP A 359 LEU A 363 1 O VAL A 360 N ARG A 340 SHEET 1 AA2 3 PRO A 262 PRO A 264 0 SHEET 2 AA2 3 GLY A 249 CYS A 256 -1 N ALA A 254 O PHE A 263 SHEET 3 AA2 3 VAL A 287 ILE A 291 -1 O ASP A 290 N SER A 253 SHEET 1 AA3 2 LYS D 3 ALY D 4 0 SHEET 2 AA3 2 GLU H 296 PRO H 297 -1 O GLU H 296 N ALY D 4 SHEET 1 AA4 6 LEU H 244 GLU H 246 0 SHEET 2 AA4 6 LEU H 222 THR H 227 1 N THR H 227 O VAL H 245 SHEET 3 AA4 6 VAL H 140 VAL H 144 1 N VAL H 140 O LEU H 223 SHEET 4 AA4 6 LEU H 314 LEU H 318 1 O LEU H 316 N MET H 143 SHEET 5 AA4 6 ARG H 340 ASN H 344 1 O LEU H 341 N ILE H 317 SHEET 6 AA4 6 VAL H 360 LEU H 363 1 O GLN H 362 N LEU H 342 SHEET 1 AA5 3 PRO H 262 PRO H 264 0 SHEET 2 AA5 3 GLY H 249 CYS H 256 -1 N ALA H 254 O PHE H 263 SHEET 3 AA5 3 VAL H 287 ILE H 291 -1 O ASP H 290 N SER H 253 LINK C LYS D 3 N ALY D 4 1555 1555 1.27 LINK C ALY D 4 N MCM D 101 1555 1555 1.34 LINK C LYS C 3 N ALY C 4 1555 1555 1.26 LINK C ALY C 4 N MCM C 101 1555 1555 1.35 LINK SG CYS A 256 ZN ZN A 401 1555 1555 2.27 LINK SG CYS A 280 ZN ZN A 401 1555 1555 2.32 LINK SG CYS A 283 ZN ZN A 401 1555 1555 2.06 LINK SG CYS H 256 ZN ZN H 402 1555 1555 2.20 LINK SG CYS H 259 ZN ZN H 402 1555 1555 2.13 LINK SG CYS H 280 ZN ZN H 402 1555 1555 2.72 LINK SG CYS H 283 ZN ZN H 402 1555 1555 2.98 CISPEP 1 GLU A 325 PRO A 326 0 6.71 CISPEP 2 GLU H 325 PRO H 326 0 -0.65 SITE 1 AC1 4 CYS A 256 CYS A 259 CYS A 280 CYS A 283 SITE 1 AC2 9 PHE A 157 ARG A 158 GLU A 177 PHE A 294 SITE 2 AC2 9 VAL A 324 ARG D 1 HIS D 2 PRO H 326 SITE 3 AC2 9 SER H 329 SITE 1 AC3 17 GLY A 145 ALA A 146 GLY A 147 SER A 149 SITE 2 AC3 17 THR A 150 PHE A 157 ARG A 158 GLN A 228 SITE 3 AC3 17 ASN A 229 ILE A 230 ASP A 231 HIS A 248 SITE 4 AC3 17 GLY A 319 THR A 320 SER A 321 ASP A 365 SITE 5 AC3 17 VAL A 366 SITE 1 AC5 7 ARG H 224 ALA H 241 SER H 242 LYS H 243 SITE 2 AC5 7 LEU H 244 VAL H 245 ARG H 301 SITE 1 AC6 4 CYS H 256 CYS H 259 CYS H 280 CYS H 283 SITE 1 AC7 8 PRO A 326 SER A 329 ARG C 1 ARG H 158 SITE 2 AC7 8 GLU H 177 PHE H 294 VAL H 324 NAD H 406 SITE 1 AC8 18 GLY H 145 ALA H 146 GLY H 147 SER H 149 SITE 2 AC8 18 THR H 150 PRO H 151 ARG H 158 GLN H 228 SITE 3 AC8 18 ASN H 229 ILE H 230 ASP H 231 HIS H 248 SITE 4 AC8 18 THR H 320 SER H 321 ASN H 344 ASP H 365 SITE 5 AC8 18 VAL H 366 BBI H 405 CRYST1 114.560 114.560 123.404 90.00 90.00 120.00 H 3 18 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 0.008729 0.005040 0.000000 0.00000 SCALE2 0.000000 0.010079 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008103 0.00000