HEADER HYDROLASE/DNA 23-OCT-06 2NMV
TITLE DAMAGE DETECTION BY THE UVRABC PATHWAY: CRYSTAL STRUCTURE OF UVRB
TITLE 2 BOUND TO FLUORESCEIN-ADDUCTED DNA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(P*TP*TP*TP*TP*T)-3';
COMPND 3 CHAIN: D;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: UVRABC SYSTEM PROTEIN B;
COMPND 7 CHAIN: A;
COMPND 8 SYNONYM: PROTEIN UVRB, EXCINUCLEASE ABC SUBUNIT B, PROTEIN DINA;
COMPND 9 EC: 3.1.-.-;
COMPND 10 ENGINEERED: YES;
COMPND 11 MOL_ID: 3;
COMPND 12 MOLECULE: UVRABC SYSTEM PROTEIN B;
COMPND 13 CHAIN: B;
COMPND 14 FRAGMENT: RESIDUES 622-659;
COMPND 15 SYNONYM: PROTEIN UVRB, EXCINUCLEASE ABC SUBUNIT B, PROTEIN DINA;
COMPND 16 EC: 3.1.-.-;
COMPND 17 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS;
SOURCE 5 ORGANISM_TAXID: 1423;
SOURCE 6 GENE: UVRB;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21DE3 PLYSS;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET8C;
SOURCE 12 MOL_ID: 3;
SOURCE 13 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS;
SOURCE 14 ORGANISM_TAXID: 1423;
SOURCE 15 GENE: UVRB;
SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21DE3 PLYSS;
SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET8C
KEYWDS PROTEIN-DNA COMPLEX, T-FLUORESCEIN, HAIRPIN, HYDROLASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR T.R.WATERS,J.ERYILMAZ,S.GEDDES,T.E.BARRETT
REVDAT 3 25-OCT-23 2NMV 1 REMARK LINK
REVDAT 2 24-FEB-09 2NMV 1 VERSN
REVDAT 1 16-JAN-07 2NMV 0
JRNL AUTH T.R.WATERS,J.ERYILMAZ,S.GEDDES,T.E.BARRETT
JRNL TITL DAMAGE DETECTION BY THE UVRABC PATHWAY: CRYSTAL STRUCTURE OF
JRNL TITL 2 UVRB BOUND TO FLUORESCEIN-ADDUCTED DNA
JRNL REF FEBS LETT. V. 580 6423 2006
JRNL REFN ISSN 0014-5793
JRNL PMID 17097086
JRNL DOI 10.1016/J.FEBSLET.2006.10.051
REMARK 2
REMARK 2 RESOLUTION. 2.95 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0005
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) : 2.95
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.36
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8
REMARK 3 NUMBER OF REFLECTIONS : 14309
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) : 0.227
REMARK 3 R VALUE (WORKING SET) : 0.224
REMARK 3 FREE R VALUE : 0.281
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 755
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) : 2.95
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.03
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1010
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.17
REMARK 3 BIN R VALUE (WORKING SET) : 0.2650
REMARK 3 BIN FREE R VALUE SET COUNT : 71
REMARK 3 BIN FREE R VALUE : 0.3590
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5179
REMARK 3 NUCLEIC ACID ATOMS : 84
REMARK 3 HETEROGEN ATOMS : 48
REMARK 3 SOLVENT ATOMS : 0
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 73.70
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.35
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.21000
REMARK 3 B22 (A**2) : -2.04000
REMARK 3 B33 (A**2) : 0.82000
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): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.515
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.400
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.806
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.901
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.852
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5403 ; 0.016 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7315 ; 1.713 ; 2.002
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 654 ; 6.527 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 260 ;36.008 ;24.038
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 938 ;20.405 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 47 ;18.861 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 829 ; 0.101 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4055 ; 0.005 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2515 ; 0.246 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3670 ; 0.323 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 182 ; 0.169 ; 0.200
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): 80 ; 0.243 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.181 ; 0.200
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): 3356 ; 0.696 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5264 ; 1.234 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2317 ; 1.799 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2051 ; 3.052 ; 4.500
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 : 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
REMARK 4
REMARK 4 2NMV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-OCT-06.
REMARK 100 THE DEPOSITION ID IS D_1000040055.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-DEC-05
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID23-2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.980
REMARK 200 MONOCHROMATOR : SI 111 CHANNEL
REMARK 200 OPTICS : BENT CYLINDRICAL MIRROR
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA)
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15109
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.950
REMARK 200 RESOLUTION RANGE LOW (A) : 68.360
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 200 DATA REDUNDANCY : 5.300
REMARK 200 R MERGE (I) : 0.09400
REMARK 200 R SYM (I) : 0.09400
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.95
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.03
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3
REMARK 200 DATA REDUNDANCY IN SHELL : 5.50
REMARK 200 R MERGE FOR SHELL (I) : 0.36900
REMARK 200 R SYM FOR SHELL (I) : 0.36900
REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.200
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 2D7D
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 41.74
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 18-20% PEG 20000, 0.1M PH 8.5 TRIS
REMARK 280 -HCL, MICROBATCH, TEMPERATURE 289K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 37.20500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.93900
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.79850
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.93900
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.20500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.79850
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
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: TRIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, A, 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 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 MET A 1
REMARK 465 LYS A 2
REMARK 465 SER A 9
REMARK 465 LYS A 590
REMARK 465 GLU A 591
REMARK 465 ILE A 592
REMARK 465 ARG A 593
REMARK 465 ASP A 594
REMARK 465 VAL A 595
REMARK 465 ILE A 596
REMARK 465 ARG A 597
REMARK 465 ALA A 598
REMARK 465 THR A 599
REMARK 465 VAL A 600
REMARK 465 ALA A 601
REMARK 465 ALA A 602
REMARK 465 GLU A 603
REMARK 465 ASP A 604
REMARK 465 LYS A 605
REMARK 465 ALA A 606
REMARK 465 GLU A 607
REMARK 465 TYR A 608
REMARK 465 LYS A 609
REMARK 465 THR A 610
REMARK 465 LYS A 611
REMARK 465 ALA A 612
REMARK 465 ALA A 613
REMARK 465 PRO A 614
REMARK 465 LYS A 615
REMARK 465 LEU A 616
REMARK 465 SER A 617
REMARK 465 LYS A 618
REMARK 465 MET A 619
REMARK 465 THR A 620
REMARK 465 LEU A 655
REMARK 465 GLU A 656
REMARK 465 LEU A 657
REMARK 465 LYS A 658
REMARK 465 ALA A 659
REMARK 465 GLU A 660
REMARK 465 GLY A 661
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 DT D 5 C5' C4' O4' C3' O3' C2' C1'
REMARK 470 DT D 5 N1 C2 O2 N3 C4 O4 C5
REMARK 470 DT D 5 C7 C6
REMARK 470 ARG A 4 CG CD NE CZ NH1 NH2
REMARK 470 ASP A 94 CG OD1 OD2
REMARK 470 TYR A 95 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 470 GLN A 104 CG CD OE1 NE2
REMARK 470 LYS A 111 CG CD CE NZ
REMARK 470 GLU A 153 CB CG CD OE1 OE2
REMARK 470 ARG A 155 CG CD NE CZ NH1 NH2
REMARK 470 MET A 157 CG SD CE
REMARK 470 GLU A 166 CG CD OE1 OE2
REMARK 470 ILE A 186 CG1 CG2 CD1
REMARK 470 LEU A 230 CG CD1 CD2
REMARK 470 PHE A 249 CG CD1 CD2 CE1 CE2 CZ
REMARK 470 GLU A 254 CG CD OE1 OE2
REMARK 470 LYS A 255 CG CD CE NZ
REMARK 470 GLU A 257 CG CD OE1 OE2
REMARK 470 GLN A 284 CG CD OE1 NE2
REMARK 470 GLU A 295 CG CD OE1 OE2
REMARK 470 GLU A 406 CG CD OE1 OE2
REMARK 470 LYS A 455 CG CD CE NZ
REMARK 470 LYS A 456 CG CD CE NZ
REMARK 470 GLU A 467 CG CD OE1 OE2
REMARK 470 HIS A 476 CG ND1 CD2 CE1 NE2
REMARK 470 GLU A 478 CG CD OE1 OE2
REMARK 470 LYS A 480 CG CD CE NZ
REMARK 470 ARG A 484 CG CD NE CZ NH1 NH2
REMARK 470 ARG A 489 CG CD NE CZ NH1 NH2
REMARK 470 ARG A 506 CG CD NE CZ NH1 NH2
REMARK 470 LYS A 586 CG CD CE NZ
REMARK 470 ASN A 589 CG OD1 ND2
REMARK 470 LYS A 621 CG CD CE NZ
REMARK 470 LYS A 622 CG CD CE NZ
REMARK 470 GLU A 623 CG CD OE1 OE2
REMARK 470 ARG A 624 CG CD NE CZ NH1 NH2
REMARK 470 GLN A 625 CG CD OE1 NE2
REMARK 470 LYS A 626 CG CD CE NZ
REMARK 470 VAL A 627 CG1 CG2
REMARK 470 GLU A 629 CG CD OE1 OE2
REMARK 470 GLN A 630 CG CD OE1 NE2
REMARK 470 GLU A 634 CG CD OE1 OE2
REMARK 470 LYS A 636 CG CD CE NZ
REMARK 470 LYS B 622 CG CD CE NZ
REMARK 470 GLN B 625 CG CD OE1 NE2
REMARK 470 LYS B 636 CG CD CE NZ
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 DT D 3 C6 DT D 3 N1 -0.045
REMARK 500 DT D 3 C5 DT D 3 C7 0.068
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 DT D 1 O4' - C1' - N1 ANGL. DEV. = 9.5 DEGREES
REMARK 500 DT D 2 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 DT D 3 O3' - P - O5' ANGL. DEV. = -16.4 DEGREES
REMARK 500 DT D 3 O3' - P - OP2 ANGL. DEV. = 21.7 DEGREES
REMARK 500 DT D 3 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DT D 3 N1 - C2 - N3 ANGL. DEV. = 4.7 DEGREES
REMARK 500 DT D 3 C2 - N3 - C4 ANGL. DEV. = -7.0 DEGREES
REMARK 500 DT D 3 N3 - C4 - C5 ANGL. DEV. = 5.5 DEGREES
REMARK 500 DT D 3 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES
REMARK 500 DT D 3 C4 - C5 - C7 ANGL. DEV. = 4.2 DEGREES
REMARK 500 DT D 3 C3' - O3' - P ANGL. DEV. = -12.9 DEGREES
REMARK 500 DT D 4 O3' - P - O5' ANGL. DEV. = -19.4 DEGREES
REMARK 500 DT D 4 O3' - P - OP2 ANGL. DEV. = 10.3 DEGREES
REMARK 500 ASP A 120 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES
REMARK 500 PRO A 317 C - N - CA ANGL. DEV. = 9.4 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 PRO A 13 119.14 -35.92
REMARK 500 ALA A 113 128.71 -174.66
REMARK 500 SER A 141 -159.50 -89.47
REMARK 500 ILE A 167 130.32 173.12
REMARK 500 GLN A 180 14.54 81.30
REMARK 500 GLU A 209 -42.94 -144.27
REMARK 500 ASP A 219 62.89 -106.86
REMARK 500 LEU A 315 19.98 54.62
REMARK 500 HIS A 387 -77.05 -76.88
REMARK 500 SER A 393 137.90 -172.58
REMARK 500 LEU A 417 126.62 -34.40
REMARK 500 GLN A 430 -69.27 -21.85
REMARK 500 ASN A 445 56.55 33.08
REMARK 500 ILE A 502 -61.33 -94.76
REMARK 500 GLU A 525 -126.83 52.65
REMARK 500 GLU A 579 -70.57 -55.02
REMARK 500 GLU A 580 -17.89 -48.21
REMARK 500 PRO A 585 100.31 -44.75
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 FLU D 600
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 662
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NML D 103
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FLU D 600
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2D7D RELATED DB: PDB
REMARK 900 THE SAME PROTEIN COMPLEXED WITH FLUORESCEIN ADDUCTED PENTATHYMINE
DBREF 2NMV A 1 661 UNP P37954 UVRB_BACSU 1 661
DBREF 2NMV B 622 659 UNP P37954 UVRB_BACSU 622 659
DBREF 2NMV D 1 5 PDB 2NMV 2NMV 1 5
SEQRES 1 D 5 DT DT DT DT DT
SEQRES 1 A 661 MET LYS ASP ARG PHE GLU LEU VAL SER LYS TYR GLN PRO
SEQRES 2 A 661 GLN GLY ASP GLN PRO LYS ALA ILE GLU LYS LEU VAL LYS
SEQRES 3 A 661 GLY ILE GLN GLU GLY LYS LYS HIS GLN THR LEU LEU GLY
SEQRES 4 A 661 ALA THR GLY THR GLY LYS THR PHE THR VAL SER ASN LEU
SEQRES 5 A 661 ILE LYS GLU VAL ASN LYS PRO THR LEU VAL ILE ALA HIS
SEQRES 6 A 661 ASN LYS THR LEU ALA GLY GLN LEU TYR SER GLU PHE LYS
SEQRES 7 A 661 GLU PHE PHE PRO ASN ASN ALA VAL GLU TYR PHE VAL SER
SEQRES 8 A 661 TYR TYR ASP TYR TYR GLN PRO GLU ALA TYR VAL PRO GLN
SEQRES 9 A 661 THR ASP THR PHE ILE GLU LYS ASP ALA SER ILE ASN ASP
SEQRES 10 A 661 GLU ILE ASP LYS LEU ARG HIS SER ALA THR SER ALA LEU
SEQRES 11 A 661 PHE GLU ARG ARG ASP VAL ILE ILE ILE ALA SER VAL SER
SEQRES 12 A 661 CYS ILE TYR GLY LEU GLY SER PRO GLU GLU TYR ARG GLU
SEQRES 13 A 661 MET VAL VAL SER LEU ARG THR GLU MET GLU ILE GLU ARG
SEQRES 14 A 661 ASN GLU LEU LEU ARG LYS LEU VAL ASP ILE GLN TYR ALA
SEQRES 15 A 661 ARG ASN ASP ILE ASP PHE GLN ARG GLY THR PHE ARG VAL
SEQRES 16 A 661 ARG GLY ASP VAL VAL GLU ILE PHE PRO ALA SER ARG ASP
SEQRES 17 A 661 GLU HIS CYS VAL ARG VAL GLU PHE PHE GLY ASP GLU ILE
SEQRES 18 A 661 GLU ARG ILE ARG GLU VAL ASP ALA LEU THR GLY GLU ILE
SEQRES 19 A 661 LEU GLY ASP ARG ASP HIS VAL ALA ILE PHE PRO ALA SER
SEQRES 20 A 661 HIS PHE VAL THR ARG ALA GLU LYS MET GLU LYS ALA ILE
SEQRES 21 A 661 GLN ASN ILE GLU LYS GLU LEU GLU GLU GLN LEU LYS VAL
SEQRES 22 A 661 MET HIS GLU ASN GLY LYS LEU LEU GLU ALA GLN ARG LEU
SEQRES 23 A 661 GLU GLN ARG THR ARG TYR ASP LEU GLU MET MET ARG GLU
SEQRES 24 A 661 MET GLY PHE CYS SER GLY ILE GLU ASN TYR SER ARG HIS
SEQRES 25 A 661 LEU THR LEU ARG PRO PRO GLY SER THR PRO TYR THR LEU
SEQRES 26 A 661 LEU ASP TYR PHE PRO ASP ASP PHE MET ILE VAL VAL ASP
SEQRES 27 A 661 GLU SER HIS VAL THR ILE PRO GLN VAL ARG GLY MET PHE
SEQRES 28 A 661 ASN GLY ASP GLN ALA ARG LYS GLN VAL LEU VAL ASP HIS
SEQRES 29 A 661 GLY PHE ARG LEU PRO SER ALA LEU ASP ASN ARG PRO LEU
SEQRES 30 A 661 ARG PHE GLU GLU PHE GLU LYS HIS MET HIS ASN ILE VAL
SEQRES 31 A 661 TYR VAL SER ALA THR PRO GLY PRO TYR GLU ILE GLU HIS
SEQRES 32 A 661 THR ASP GLU MET VAL GLU GLN ILE ILE ARG PRO THR GLY
SEQRES 33 A 661 LEU LEU ASP PRO LEU ILE ASP VAL ARG PRO ILE GLU GLY
SEQRES 34 A 661 GLN ILE ASP ASP LEU ILE GLY GLU ILE GLN ALA ARG ILE
SEQRES 35 A 661 GLU ARG ASN GLU ARG VAL LEU VAL THR THR LEU THR LYS
SEQRES 36 A 661 LYS MET SER GLU ASP LEU THR ASP TYR LEU LYS GLU ILE
SEQRES 37 A 661 GLY ILE LYS VAL ASN TYR LEU HIS SER GLU ILE LYS THR
SEQRES 38 A 661 LEU GLU ARG ILE GLU ILE ILE ARG ASP LEU ARG LEU GLY
SEQRES 39 A 661 LYS TYR ASP VAL LEU VAL GLY ILE ASN LEU LEU ARG GLU
SEQRES 40 A 661 GLY LEU ASP ILE PRO GLU VAL SER LEU VAL ALA ILE LEU
SEQRES 41 A 661 ASP ALA ASP LYS GLU GLY PHE LEU ARG SER GLU ARG SER
SEQRES 42 A 661 LEU ILE GLN THR ILE GLY ARG ALA ALA ARG ASN ALA GLU
SEQRES 43 A 661 GLY ARG VAL ILE MET TYR ALA ASP LYS ILE THR LYS SER
SEQRES 44 A 661 MET GLU ILE ALA ILE ASN GLU THR LYS ARG ARG ARG GLU
SEQRES 45 A 661 GLN GLN GLU ARG PHE ASN GLU GLU HIS GLY ILE THR PRO
SEQRES 46 A 661 LYS THR ILE ASN LYS GLU ILE ARG ASP VAL ILE ARG ALA
SEQRES 47 A 661 THR VAL ALA ALA GLU ASP LYS ALA GLU TYR LYS THR LYS
SEQRES 48 A 661 ALA ALA PRO LYS LEU SER LYS MET THR LYS LYS GLU ARG
SEQRES 49 A 661 GLN LYS VAL VAL GLU GLN MET GLU HIS GLU MET LYS GLU
SEQRES 50 A 661 ALA ALA LYS ALA LEU ASP PHE GLU ARG ALA ALA GLU LEU
SEQRES 51 A 661 ARG ASP LEU LEU LEU GLU LEU LYS ALA GLU GLY
SEQRES 1 B 38 LYS GLU ARG GLN LYS VAL VAL GLU GLN MET GLU HIS GLU
SEQRES 2 B 38 MET LYS GLU ALA ALA LYS ALA LEU ASP PHE GLU ARG ALA
SEQRES 3 B 38 ALA GLU LEU ARG ASP LEU LEU LEU GLU LEU LYS ALA
HET NML D 103 5
HET FLU D 600 16
HET ADP A 662 27
HETNAM NML N-METHYLACETAMIDE
HETNAM FLU 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID
HETNAM ADP ADENOSINE-5'-DIPHOSPHATE
HETSYN FLU FLUORESCEIN
FORMUL 4 NML C3 H7 N O
FORMUL 5 FLU C20 H12 O5
FORMUL 6 ADP C10 H15 N5 O10 P2
HELIX 1 1 ASP A 16 GLU A 30 1 15
HELIX 2 2 GLY A 44 ASN A 57 1 14
HELIX 3 3 ASN A 66 PHE A 81 1 16
HELIX 4 4 ASN A 116 ARG A 133 1 18
HELIX 5 5 VAL A 142 TYR A 146 5 5
HELIX 6 6 SER A 150 VAL A 158 1 9
HELIX 7 7 GLU A 168 ASP A 178 1 11
HELIX 8 8 ARG A 252 ASN A 277 1 26
HELIX 9 9 LYS A 279 GLY A 301 1 23
HELIX 10 10 GLY A 305 ASN A 308 5 4
HELIX 11 11 TYR A 309 THR A 314 1 6
HELIX 12 12 THR A 324 PHE A 329 1 6
HELIX 13 13 GLU A 339 HIS A 364 1 26
HELIX 14 14 LEU A 368 ASN A 374 5 7
HELIX 15 15 ARG A 378 LYS A 384 1 7
HELIX 16 16 GLY A 397 THR A 404 1 8
HELIX 17 17 GLY A 429 GLU A 443 1 15
HELIX 18 18 THR A 454 ILE A 468 1 15
HELIX 19 19 LYS A 480 GLY A 494 1 15
HELIX 20 20 ASP A 521 GLU A 525 5 5
HELIX 21 21 SER A 530 ARG A 540 1 11
HELIX 22 22 ALA A 541 ASN A 544 5 4
HELIX 23 23 THR A 557 GLY A 582 1 26
HELIX 24 24 LYS A 621 ALA A 641 1 21
HELIX 25 25 ASP A 643 LEU A 654 1 12
HELIX 26 26 LYS B 622 ALA B 641 1 20
HELIX 27 27 ASP B 643 ALA B 659 1 17
SHEET 1 A 7 ALA A 85 PHE A 89 0
SHEET 2 A 7 VAL A 136 ALA A 140 1 O ILE A 139 N PHE A 89
SHEET 3 A 7 THR A 60 ILE A 63 1 N VAL A 62 O ILE A 138
SHEET 4 A 7 MET A 334 ASP A 338 1 O VAL A 336 N LEU A 61
SHEET 5 A 7 ASN A 388 VAL A 392 1 O VAL A 390 N ILE A 335
SHEET 6 A 7 HIS A 34 GLY A 39 1 N LEU A 37 O TYR A 391
SHEET 7 A 7 VAL A 408 GLN A 410 1 O VAL A 408 N LEU A 38
SHEET 1 B 2 TYR A 93 GLN A 97 0
SHEET 2 B 2 ASP A 112 ILE A 115 -1 O SER A 114 N ASP A 94
SHEET 1 C 2 ALA A 100 TYR A 101 0
SHEET 2 C 2 PHE A 108 ILE A 109 -1 O ILE A 109 N ALA A 100
SHEET 1 D 2 VAL A 159 ARG A 162 0
SHEET 2 D 2 HIS A 240 ILE A 243 -1 O VAL A 241 N LEU A 161
SHEET 1 E 6 ALA A 182 ARG A 183 0
SHEET 2 E 6 THR A 192 ARG A 196 1 O PHE A 193 N ALA A 182
SHEET 3 E 6 VAL A 199 ILE A 202 -1 O GLU A 201 N ARG A 194
SHEET 4 E 6 HIS A 210 PHE A 216 -1 O VAL A 214 N VAL A 200
SHEET 5 E 6 ILE A 221 ASP A 228 -1 O GLU A 222 N GLU A 215
SHEET 6 E 6 ILE A 234 ARG A 238 -1 O LEU A 235 N GLU A 226
SHEET 1 F 6 LEU A 421 ARG A 425 0
SHEET 2 F 6 ARG A 548 TYR A 552 1 O MET A 551 N ASP A 423
SHEET 3 F 6 VAL A 514 ILE A 519 1 N ILE A 519 O ILE A 550
SHEET 4 F 6 ARG A 447 THR A 451 1 N LEU A 449 O ALA A 518
SHEET 5 F 6 VAL A 498 GLY A 501 1 O LEU A 499 N VAL A 450
SHEET 6 F 6 VAL A 472 LEU A 475 1 N LEU A 475 O VAL A 500
LINK C7 DT D 3 C1 NML D 103 1555 1555 1.57
SITE 1 AC1 13 TYR A 11 GLN A 12 GLN A 14 GLN A 17
SITE 2 AC1 13 ALA A 40 GLY A 42 THR A 43 GLY A 44
SITE 3 AC1 13 LYS A 45 THR A 46 PHE A 47 PRO A 414
SITE 4 AC1 13 ARG A 543
SITE 1 AC2 2 DT D 2 DT D 3
SITE 1 AC3 5 GLY A 71 TYR A 74 SER A 75 ASN A 116
SITE 2 AC3 5 ILE A 119
CRYST1 74.410 95.597 97.878 90.00 90.00 90.00 P 21 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 0.013439 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010461 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010217 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
