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 <I/SIGMA(I)> 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 <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: 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