HEADER LIGASE 27-JAN-04 1V9P
TITLE CRYSTAL STRUCTURE OF NAD+-DEPENDENT DNA LIGASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA LIGASE;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: POLYDEOXYRIBONUCLEOTIDE SYNTHASE [NAD+], TFI DNA LIGASE;
COMPND 5 EC: 6.5.1.2;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS FILIFORMIS;
SOURCE 3 ORGANISM_TAXID: 276;
SOURCE 4 GENE: LIGA;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS NAD+-DEPENDENT DNA LIGASE, LIGASE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.Y.LEE,C.CHANG,H.K.SONG,J.MOON,J.K.YANG,H.K.KIM,S.K.KWON,S.W.SUH
REVDAT 3 27-DEC-23 1V9P 1 REMARK LINK
REVDAT 2 24-FEB-09 1V9P 1 VERSN
REVDAT 1 30-MAR-04 1V9P 0
SPRSDE 30-MAR-04 1V9P 1DGT
JRNL AUTH J.Y.LEE,C.CHANG,H.K.SONG,J.MOON,J.K.YANG,H.K.KIM,S.T.KWON,
JRNL AUTH 2 S.W.SUH
JRNL TITL CRYSTAL STRUCTURE OF NAD(+)-DEPENDENT DNA LIGASE: MODULAR
JRNL TITL 2 ARCHITECTURE AND FUNCTIONAL IMPLICATIONS.
JRNL REF EMBO J. V. 19 1119 2000
JRNL REFN ISSN 0261-4189
JRNL PMID 10698952
JRNL DOI 10.1093/EMBOJ/19.5.1119
REMARK 2
REMARK 2 RESOLUTION. 2.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.1
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.93
REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 114413.930
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.4
REMARK 3 NUMBER OF REFLECTIONS : 36056
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 SET) : 0.232
REMARK 3 FREE R VALUE : 0.293
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000
REMARK 3 FREE R VALUE TEST SET COUNT : 3616
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 6
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.80
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4179
REMARK 3 BIN R VALUE (WORKING SET) : 0.3190
REMARK 3 BIN FREE R VALUE : 0.4020
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.50
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 489
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 9484
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 46
REMARK 3 SOLVENT ATOMS : 238
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.70
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -9.16000
REMARK 3 B22 (A**2) : 4.21000
REMARK 3 B33 (A**2) : 4.96000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 9.06000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.37
REMARK 3 ESD FROM SIGMAA (A) : 0.40
REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.50
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.60
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.009
REMARK 3 BOND ANGLES (DEGREES) : 1.500
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.60
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.920
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 7.220 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 11.460; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 8.650 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 13.070; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.30
REMARK 3 BSOL : 32.97
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM
REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 3 : ION.PARAM
REMARK 3 PARAMETER FILE 4 : AMP.PAR
REMARK 3 PARAMETER FILE 5 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : WATER.TOP
REMARK 3 TOPOLOGY FILE 3 : ION.TOP
REMARK 3 TOPOLOGY FILE 4 : AMP.TOP
REMARK 3 TOPOLOGY FILE 5 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1V9P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-04.
REMARK 100 THE DEPOSITION ID IS D_1000006382.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-JAN-99
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSLS
REMARK 200 BEAMLINE : X8C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.009
REMARK 200 MONOCHROMATOR : YALE MIRRORS
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36056
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : NULL
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.08
REMARK 200 COMPLETENESS FOR SHELL (%) : 69.8
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: MAD
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
REMARK 200 SOFTWARE USED: SOLVE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 64.21
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.46
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 5% METHOXYPEG 5000, 100MM SODIUM
REMARK 280 CITRATE(PH 5.6), 5MM CALCIUM CHLORIDE, VAPOR DIFFUSION, HANGING
REMARK 280 DROP, TEMPERATURE 295K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,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 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 58.66500
REMARK 290 SMTRY3 2 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 300 REMARK: BIOLOGICAL UNIT IS MONOMER
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: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 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 LEU A 359 N LEU A 359 CA -0.132
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 VAL A 94 CB - CA - C ANGL. DEV. = -14.8 DEGREES
REMARK 500 LEU A 105 C - N - CA ANGL. DEV. = 15.0 DEGREES
REMARK 500 LEU A 359 CB - CA - C ANGL. DEV. = 22.0 DEGREES
REMARK 500 LEU A 359 N - CA - C ANGL. DEV. = -22.9 DEGREES
REMARK 500 HIS B2360 N - CA - C ANGL. DEV. = 20.9 DEGREES
REMARK 500 HIS B2360 CA - C - N ANGL. DEV. = 20.5 DEGREES
REMARK 500 HIS B2360 O - C - N ANGL. DEV. = -10.7 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 ARG A 3 -35.25 -35.17
REMARK 500 TYR A 24 -99.90 -102.63
REMARK 500 TYR A 25 -4.24 -47.43
REMARK 500 PHE A 51 62.00 -150.29
REMARK 500 PRO A 57 8.03 -57.80
REMARK 500 GLU A 62 -6.23 -38.49
REMARK 500 GLN A 63 22.64 -164.89
REMARK 500 VAL A 64 -168.13 -41.98
REMARK 500 ALA A 66 36.41 -96.29
REMARK 500 LEU A 69 102.36 -56.80
REMARK 500 PHE A 73 38.15 -69.08
REMARK 500 VAL A 94 -16.37 84.05
REMARK 500 ARG A 103 84.20 -60.59
REMARK 500 ALA A 104 -59.37 155.06
REMARK 500 LEU A 105 -150.75 42.37
REMARK 500 ARG A 107 51.71 74.71
REMARK 500 LYS A 108 -168.62 -172.10
REMARK 500 ARG A 109 -48.08 -172.19
REMARK 500 VAL A 119 104.87 -59.00
REMARK 500 GLU A 130 13.54 47.81
REMARK 500 VAL A 148 34.11 -153.56
REMARK 500 SER A 207 -16.44 -47.59
REMARK 500 ARG A 209 51.08 -97.11
REMARK 500 LEU A 221 117.59 -7.85
REMARK 500 LEU A 230 107.55 -49.32
REMARK 500 GLU A 234 -43.86 167.19
REMARK 500 LEU A 275 -17.86 -45.12
REMARK 500 THR A 304 -158.15 -80.73
REMARK 500 ARG A 306 39.11 -145.07
REMARK 500 LEU A 326 -62.87 -91.59
REMARK 500 LEU A 359 -140.53 -82.63
REMARK 500 HIS A 360 -91.33 -142.67
REMARK 500 ILE A 372 -81.96 -89.32
REMARK 500 VAL A 384 -33.13 -148.56
REMARK 500 CYS A 412 -12.76 -168.66
REMARK 500 ALA A 446 -131.92 -90.49
REMARK 500 ASP A 448 95.89 31.76
REMARK 500 LEU A 452 84.10 -56.13
REMARK 500 ARG A 467 -29.09 -143.09
REMARK 500 ARG A 476 -48.87 -23.90
REMARK 500 LYS A 477 98.79 -55.64
REMARK 500 LEU A 483 10.04 -165.67
REMARK 500 ARG A 485 -6.53 78.06
REMARK 500 ALA A 491 -71.19 -68.16
REMARK 500 GLN A 492 -34.92 -39.53
REMARK 500 LEU A 506 -39.63 -38.44
REMARK 500 GLU A 507 -72.99 -55.19
REMARK 500 LEU A 513 20.07 -78.41
REMARK 500 PRO A 516 94.75 -54.73
REMARK 500 VAL A 518 89.92 -56.85
REMARK 500
REMARK 500 THIS ENTRY HAS 113 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 AMP A 700
REMARK 610 AMP B 2700
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 701 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 409 SG
REMARK 620 2 CYS A 412 SG 93.7
REMARK 620 3 CYS A 425 SG 102.7 92.1
REMARK 620 4 CYS A 430 SG 122.8 121.4 117.8
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B2701 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS B2409 SG
REMARK 620 2 CYS B2412 SG 112.2
REMARK 620 3 CYS B2425 SG 141.0 79.6
REMARK 620 4 CYS B2430 SG 122.2 86.4 94.6
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 701
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 2701
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP A 700
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP B 2700
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1DGT RELATED DB: PDB
REMARK 900 THE PREVIOUSLY DEPOSITED PDB COORDINATE(1DGT) HAD INCORRECT PORTION
REMARK 900 BECAUSE OF IMPERFECT AMINO ACID SEQUENCE, WHICH WAS INFORMED BY
REMARK 900 OTHER GROUP. THEREFORE, WE ARE GOING TO REPLACE THE OLD COORDINATE
REMARK 900 WITH THE NEW ONE, WHICH WAS MODIFIED ACCORDING TO THE CORRECT AMINO
REMARK 900 ACID SEQUENCE. ENTRY 1DGT IS OBSOLETED AND SUPERCEDED BY THIS ENTRY.
DBREF 1V9P A 1 584 UNP Q9ZHI0 DNLJ_THEFI 1 584
DBREF 1V9P B 2001 2584 UNP Q9ZHI0 DNLJ_THEFI 1 584
SEQRES 1 A 584 MET THR ARG GLU GLU ALA ARG ARG ARG ILE ASN GLU LEU
SEQRES 2 A 584 ARG ASP LEU ILE ARG TYR HIS ASN TYR ARG TYR TYR VAL
SEQRES 3 A 584 LEU ALA ASP PRO GLU ILE SER ASP ALA GLU TYR ASP ARG
SEQRES 4 A 584 LEU LEU ARG GLU LEU LYS GLU LEU GLU GLU ARG PHE PRO
SEQRES 5 A 584 GLU PHE LYS SER PRO ASP SER PRO THR GLU GLN VAL GLY
SEQRES 6 A 584 ALA ARG PRO LEU GLU PRO THR PHE ARG PRO VAL ARG HIS
SEQRES 7 A 584 PRO THR ARG MET TYR SER LEU ASP ASN ALA PHE THR TYR
SEQRES 8 A 584 GLU GLU VAL LEU ALA PHE GLU GLU ARG LEU GLU ARG ALA
SEQRES 9 A 584 LEU GLY ARG LYS ARG PRO PHE LEU TYR THR VAL GLU HIS
SEQRES 10 A 584 LYS VAL ASP GLY LEU SER VAL ASN LEU TYR TYR GLU GLU
SEQRES 11 A 584 GLY VAL LEU VAL PHE GLY ALA THR ARG GLY ASP GLY GLU
SEQRES 12 A 584 VAL GLY GLU GLU VAL THR GLN ASN LEU LEU THR ILE PRO
SEQRES 13 A 584 THR ILE PRO ARG ARG LEU LYS GLY VAL PRO ASP ARG LEU
SEQRES 14 A 584 GLU VAL ARG GLY GLU VAL TYR MET PRO ILE GLU ALA PHE
SEQRES 15 A 584 LEU ARG LEU ASN GLU GLU LEU GLU GLU ARG GLY GLU LYS
SEQRES 16 A 584 VAL PHE LYS ASN PRO ARG ASN ALA ALA ALA GLY SER LEU
SEQRES 17 A 584 ARG GLN LYS ASP PRO ARG VAL THR ALA LYS ARG GLY LEU
SEQRES 18 A 584 ARG ALA THR PHE TYR ALA LEU GLY LEU GLY LEU GLU GLU
SEQRES 19 A 584 SER GLY LEU LYS SER GLN TYR GLU LEU LEU LEU TRP LEU
SEQRES 20 A 584 LYS GLU LYS GLY PHE PRO VAL GLU HIS GLY TYR GLU LYS
SEQRES 21 A 584 ALA LEU GLY ALA GLU GLY VAL GLU GLU VAL TYR ARG ARG
SEQRES 22 A 584 PHE LEU ALA GLN ARG HIS ALA LEU PRO PHE GLU ALA ASP
SEQRES 23 A 584 GLY VAL VAL VAL LYS LEU ASP ASP LEU ALA LEU TRP ARG
SEQRES 24 A 584 GLU LEU GLY TYR THR ALA ARG ALA PRO ARG PHE ALA LEU
SEQRES 25 A 584 ALA TYR LYS PHE PRO ALA GLU GLU LYS GLU THR ARG LEU
SEQRES 26 A 584 LEU ASP VAL VAL PHE GLN VAL GLY ARG THR GLY ARG VAL
SEQRES 27 A 584 THR PRO VAL GLY VAL LEU GLU PRO VAL PHE ILE GLU GLY
SEQRES 28 A 584 SER GLU VAL SER ARG VAL THR LEU HIS ASN GLU SER TYR
SEQRES 29 A 584 ILE GLU GLU LEU ASP ILE ARG ILE GLY ASP TRP VAL LEU
SEQRES 30 A 584 VAL HIS LYS ALA GLY GLY VAL ILE PRO GLU VAL LEU ARG
SEQRES 31 A 584 VAL LEU LYS GLU ARG ARG THR GLY GLU GLU ARG PRO ILE
SEQRES 32 A 584 ARG TRP PRO GLU THR CYS PRO GLU CYS GLY HIS ARG LEU
SEQRES 33 A 584 VAL LYS GLU GLY LYS VAL HIS ARG CYS PRO ASN PRO LEU
SEQRES 34 A 584 CYS PRO ALA LYS ARG PHE GLU ALA ILE ARG HIS TYR ALA
SEQRES 35 A 584 SER ARG LYS ALA MET ASP ILE GLU GLY LEU GLY GLU LYS
SEQRES 36 A 584 LEU ILE GLU ARG LEU LEU GLU LYS GLY LEU VAL ARG ASP
SEQRES 37 A 584 VAL ALA ASP LEU TYR HIS LEU ARG LYS GLU ASP LEU LEU
SEQRES 38 A 584 GLY LEU GLU ARG MET GLY GLU LYS SER ALA GLN ASN LEU
SEQRES 39 A 584 LEU ARG GLN ILE GLU GLU SER LYS HIS ARG GLY LEU GLU
SEQRES 40 A 584 ARG LEU LEU TYR ALA LEU GLY LEU PRO GLY VAL GLY GLU
SEQRES 41 A 584 VAL LEU ALA ARG ASN LEU ALA ARG ARG PHE GLY THR MET
SEQRES 42 A 584 ASP ARG LEU LEU GLU ALA SER LEU GLU GLU LEU LEU GLU
SEQRES 43 A 584 VAL GLU GLU VAL GLY GLU LEU THR ALA ARG ALA ILE LEU
SEQRES 44 A 584 GLU THR LEU LYS ASP PRO ALA PHE ARG ASP LEU VAL ARG
SEQRES 45 A 584 ARG LEU LYS GLU ALA GLY VAL SER MET GLU SER LYS
SEQRES 1 B 584 MET THR ARG GLU GLU ALA ARG ARG ARG ILE ASN GLU LEU
SEQRES 2 B 584 ARG ASP LEU ILE ARG TYR HIS ASN TYR ARG TYR TYR VAL
SEQRES 3 B 584 LEU ALA ASP PRO GLU ILE SER ASP ALA GLU TYR ASP ARG
SEQRES 4 B 584 LEU LEU ARG GLU LEU LYS GLU LEU GLU GLU ARG PHE PRO
SEQRES 5 B 584 GLU PHE LYS SER PRO ASP SER PRO THR GLU GLN VAL GLY
SEQRES 6 B 584 ALA ARG PRO LEU GLU PRO THR PHE ARG PRO VAL ARG HIS
SEQRES 7 B 584 PRO THR ARG MET TYR SER LEU ASP ASN ALA PHE THR TYR
SEQRES 8 B 584 GLU GLU VAL LEU ALA PHE GLU GLU ARG LEU GLU ARG ALA
SEQRES 9 B 584 LEU GLY ARG LYS ARG PRO PHE LEU TYR THR VAL GLU HIS
SEQRES 10 B 584 LYS VAL ASP GLY LEU SER VAL ASN LEU TYR TYR GLU GLU
SEQRES 11 B 584 GLY VAL LEU VAL PHE GLY ALA THR ARG GLY ASP GLY GLU
SEQRES 12 B 584 VAL GLY GLU GLU VAL THR GLN ASN LEU LEU THR ILE PRO
SEQRES 13 B 584 THR ILE PRO ARG ARG LEU LYS GLY VAL PRO ASP ARG LEU
SEQRES 14 B 584 GLU VAL ARG GLY GLU VAL TYR MET PRO ILE GLU ALA PHE
SEQRES 15 B 584 LEU ARG LEU ASN GLU GLU LEU GLU GLU ARG GLY GLU LYS
SEQRES 16 B 584 VAL PHE LYS ASN PRO ARG ASN ALA ALA ALA GLY SER LEU
SEQRES 17 B 584 ARG GLN LYS ASP PRO ARG VAL THR ALA LYS ARG GLY LEU
SEQRES 18 B 584 ARG ALA THR PHE TYR ALA LEU GLY LEU GLY LEU GLU GLU
SEQRES 19 B 584 SER GLY LEU LYS SER GLN TYR GLU LEU LEU LEU TRP LEU
SEQRES 20 B 584 LYS GLU LYS GLY PHE PRO VAL GLU HIS GLY TYR GLU LYS
SEQRES 21 B 584 ALA LEU GLY ALA GLU GLY VAL GLU GLU VAL TYR ARG ARG
SEQRES 22 B 584 PHE LEU ALA GLN ARG HIS ALA LEU PRO PHE GLU ALA ASP
SEQRES 23 B 584 GLY VAL VAL VAL LYS LEU ASP ASP LEU ALA LEU TRP ARG
SEQRES 24 B 584 GLU LEU GLY TYR THR ALA ARG ALA PRO ARG PHE ALA LEU
SEQRES 25 B 584 ALA TYR LYS PHE PRO ALA GLU GLU LYS GLU THR ARG LEU
SEQRES 26 B 584 LEU ASP VAL VAL PHE GLN VAL GLY ARG THR GLY ARG VAL
SEQRES 27 B 584 THR PRO VAL GLY VAL LEU GLU PRO VAL PHE ILE GLU GLY
SEQRES 28 B 584 SER GLU VAL SER ARG VAL THR LEU HIS ASN GLU SER TYR
SEQRES 29 B 584 ILE GLU GLU LEU ASP ILE ARG ILE GLY ASP TRP VAL LEU
SEQRES 30 B 584 VAL HIS LYS ALA GLY GLY VAL ILE PRO GLU VAL LEU ARG
SEQRES 31 B 584 VAL LEU LYS GLU ARG ARG THR GLY GLU GLU ARG PRO ILE
SEQRES 32 B 584 ARG TRP PRO GLU THR CYS PRO GLU CYS GLY HIS ARG LEU
SEQRES 33 B 584 VAL LYS GLU GLY LYS VAL HIS ARG CYS PRO ASN PRO LEU
SEQRES 34 B 584 CYS PRO ALA LYS ARG PHE GLU ALA ILE ARG HIS TYR ALA
SEQRES 35 B 584 SER ARG LYS ALA MET ASP ILE GLU GLY LEU GLY GLU LYS
SEQRES 36 B 584 LEU ILE GLU ARG LEU LEU GLU LYS GLY LEU VAL ARG ASP
SEQRES 37 B 584 VAL ALA ASP LEU TYR HIS LEU ARG LYS GLU ASP LEU LEU
SEQRES 38 B 584 GLY LEU GLU ARG MET GLY GLU LYS SER ALA GLN ASN LEU
SEQRES 39 B 584 LEU ARG GLN ILE GLU GLU SER LYS HIS ARG GLY LEU GLU
SEQRES 40 B 584 ARG LEU LEU TYR ALA LEU GLY LEU PRO GLY VAL GLY GLU
SEQRES 41 B 584 VAL LEU ALA ARG ASN LEU ALA ARG ARG PHE GLY THR MET
SEQRES 42 B 584 ASP ARG LEU LEU GLU ALA SER LEU GLU GLU LEU LEU GLU
SEQRES 43 B 584 VAL GLU GLU VAL GLY GLU LEU THR ALA ARG ALA ILE LEU
SEQRES 44 B 584 GLU THR LEU LYS ASP PRO ALA PHE ARG ASP LEU VAL ARG
SEQRES 45 B 584 ARG LEU LYS GLU ALA GLY VAL SER MET GLU SER LYS
HET ZN A 701 1
HET AMP A 700 22
HET ZN B2701 1
HET AMP B2700 22
HETNAM ZN ZINC ION
HETNAM AMP ADENOSINE MONOPHOSPHATE
FORMUL 3 ZN 2(ZN 2+)
FORMUL 4 AMP 2(C10 H14 N5 O7 P)
FORMUL 7 HOH *238(H2 O)
HELIX 1 1 THR A 2 VAL A 26 1 25
HELIX 2 2 TYR A 37 PHE A 51 1 15
HELIX 3 3 PRO A 52 LYS A 55 5 4
HELIX 4 4 PRO A 60 VAL A 64 5 5
HELIX 5 5 LEU A 95 ARG A 103 1 9
HELIX 6 6 GLN A 150 THR A 154 5 5
HELIX 7 7 PRO A 178 GLY A 193 1 16
HELIX 8 8 ARG A 201 ARG A 209 1 9
HELIX 9 9 ASP A 212 ALA A 217 1 6
HELIX 10 10 SER A 239 LYS A 250 1 12
HELIX 11 11 GLY A 263 ALA A 276 1 14
HELIX 12 12 ASP A 294 ARG A 299 5 6
HELIX 13 13 ASN A 361 LEU A 368 1 8
HELIX 14 14 GLY A 382 VAL A 384 5 3
HELIX 15 15 LYS A 393 ARG A 396 5 4
HELIX 16 16 CYS A 430 ALA A 432 5 3
HELIX 17 17 LYS A 433 SER A 443 1 11
HELIX 18 18 GLY A 453 LYS A 463 1 11
HELIX 19 19 VAL A 469 LEU A 475 5 7
HELIX 20 20 SER A 490 SER A 501 1 12
HELIX 21 21 LYS A 502 ARG A 504 5 3
HELIX 22 22 GLY A 505 LEU A 513 1 9
HELIX 23 23 GLY A 519 ARG A 528 1 10
HELIX 24 24 THR A 532 GLU A 538 1 7
HELIX 25 25 SER A 540 GLU A 546 1 7
HELIX 26 26 GLY A 551 ASP A 564 1 14
HELIX 27 27 ASP A 564 GLU A 576 1 13
HELIX 28 28 THR B 2002 VAL B 2026 1 25
HELIX 29 29 SER B 2033 PHE B 2051 1 19
HELIX 30 30 PRO B 2052 LYS B 2055 5 4
HELIX 31 31 SER B 2059 GLN B 2063 5 5
HELIX 32 32 THR B 2090 GLU B 2102 1 13
HELIX 33 33 VAL B 2148 LEU B 2153 1 6
HELIX 34 34 PRO B 2178 ARG B 2192 1 15
HELIX 35 35 ASN B 2199 ARG B 2209 1 11
HELIX 36 36 ASP B 2212 ALA B 2217 1 6
HELIX 37 37 SER B 2239 LYS B 2250 1 12
HELIX 38 38 GLY B 2263 ARG B 2278 1 16
HELIX 39 39 HIS B 2279 LEU B 2281 5 3
HELIX 40 40 LEU B 2295 LEU B 2301 1 7
HELIX 41 41 ASN B 2361 LEU B 2368 1 8
HELIX 42 42 GLY B 2382 VAL B 2384 5 3
HELIX 43 43 LYS B 2393 ARG B 2396 5 4
HELIX 44 44 CYS B 2430 ALA B 2432 5 3
HELIX 45 45 LYS B 2433 SER B 2443 1 11
HELIX 46 46 GLY B 2453 GLY B 2464 1 12
HELIX 47 47 ASP B 2468 ARG B 2476 5 9
HELIX 48 48 LYS B 2477 GLY B 2482 1 6
HELIX 49 49 SER B 2490 ILE B 2498 1 9
HELIX 50 50 GLU B 2500 ARG B 2504 5 5
HELIX 51 51 GLY B 2505 GLY B 2514 1 10
HELIX 52 52 GLY B 2519 GLY B 2531 1 13
HELIX 53 53 THR B 2532 LEU B 2537 1 6
HELIX 54 54 SER B 2540 GLU B 2546 1 7
HELIX 55 55 GLY B 2551 LYS B 2563 1 13
HELIX 56 56 ASP B 2564 ALA B 2577 1 14
SHEET 1 A 2 PRO A 75 ARG A 77 0
SHEET 2 A 2 VAL A 144 GLU A 146 -1 O GLY A 145 N VAL A 76
SHEET 1 B 5 ASN A 87 ALA A 88 0
SHEET 2 B 5 ALA A 311 LYS A 315 1 O ALA A 313 N ALA A 88
SHEET 3 B 5 ALA A 285 LEU A 292 -1 N VAL A 288 O TYR A 314
SHEET 4 B 5 LEU A 112 VAL A 119 -1 N GLU A 116 O VAL A 289
SHEET 5 B 5 TYR A 258 LEU A 262 -1 O GLU A 259 N VAL A 115
SHEET 1 C 4 VAL A 132 THR A 138 0
SHEET 2 C 4 LEU A 122 GLU A 129 -1 N ASN A 125 O ALA A 137
SHEET 3 C 4 ARG A 168 TYR A 176 -1 O LEU A 169 N TYR A 128
SHEET 4 C 4 ARG A 222 LEU A 228 -1 O ARG A 222 N TYR A 176
SHEET 1 D 5 SER A 352 THR A 358 0
SHEET 2 D 5 VAL A 338 ILE A 349 -1 N GLY A 342 O VAL A 357
SHEET 3 D 5 LYS A 321 VAL A 332 -1 N ASP A 327 O VAL A 343
SHEET 4 D 5 TRP A 375 ALA A 381 -1 O VAL A 376 N THR A 323
SHEET 5 D 5 ILE A 385 VAL A 391 -1 O ARG A 390 N LEU A 377
SHEET 1 E 2 VAL A 417 LYS A 418 0
SHEET 2 E 2 HIS A 423 ARG A 424 -1 O ARG A 424 N VAL A 417
SHEET 1 F 2 PRO B2075 VAL B2076 0
SHEET 2 F 2 GLY B2145 GLU B2146 -1 O GLY B2145 N VAL B2076
SHEET 1 G 5 ASN B2087 ALA B2088 0
SHEET 2 G 5 ALA B2311 LYS B2315 1 O LYS B2315 N ALA B2088
SHEET 3 G 5 ALA B2285 LYS B2291 -1 N VAL B2290 O LEU B2312
SHEET 4 G 5 LEU B2112 VAL B2119 -1 N LYS B2118 O GLY B2287
SHEET 5 G 5 TYR B2258 LEU B2262 -1 O ALA B2261 N TYR B2113
SHEET 1 H 4 VAL B2132 THR B2138 0
SHEET 2 H 4 VAL B2124 GLU B2129 -1 N TYR B2127 O VAL B2134
SHEET 3 H 4 ARG B2168 GLY B2173 -1 O VAL B2171 N LEU B2126
SHEET 4 H 4 PHE B2225 LEU B2228 -1 O ALA B2227 N ARG B2172
SHEET 1 I 3 LYS B2321 ARG B2324 0
SHEET 2 I 3 TRP B2375 LYS B2380 -1 O VAL B2376 N THR B2323
SHEET 3 I 3 PRO B2386 VAL B2391 -1 O LEU B2389 N LEU B2377
SHEET 1 J 3 VAL B2329 VAL B2332 0
SHEET 2 J 3 VAL B2338 PHE B2348 -1 O THR B2339 N GLN B2331
SHEET 3 J 3 GLU B2353 THR B2358 -1 O SER B2355 N LEU B2344
LINK SG CYS A 409 ZN ZN A 701 1555 1555 2.54
LINK SG CYS A 412 ZN ZN A 701 1555 1555 2.50
LINK SG CYS A 425 ZN ZN A 701 1555 1555 2.60
LINK SG CYS A 430 ZN ZN A 701 1555 1555 2.45
LINK SG CYS B2409 ZN ZN B2701 1555 1555 2.43
LINK SG CYS B2412 ZN ZN B2701 1555 1555 2.49
LINK SG CYS B2425 ZN ZN B2701 1555 1555 2.31
LINK SG CYS B2430 ZN ZN B2701 1555 1555 2.45
SITE 1 AC1 4 CYS A 409 CYS A 412 CYS A 425 CYS A 430
SITE 1 AC2 4 CYS B2409 CYS B2412 CYS B2425 CYS B2430
SITE 1 AC3 10 LEU A 85 GLU A 116 HIS A 117 LYS A 118
SITE 2 AC3 10 VAL A 119 GLU A 174 TYR A 226 HIS A 256
SITE 3 AC3 10 LYS A 291 LYS A 315
SITE 1 AC4 10 HOH B1100 LEU B2085 ASN B2087 GLU B2116
SITE 2 AC4 10 HIS B2117 LYS B2118 VAL B2119 GLU B2174
SITE 3 AC4 10 TYR B2226 LYS B2315
CRYST1 89.210 117.330 97.480 90.00 115.09 90.00 P 1 21 1 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 0.011210 0.000000 0.005249 0.00000
SCALE2 0.000000 0.008523 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011327 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
