HEADER HYDROLASE/DNA 23-OCT-06 2NMV TITLE DAMAGE DETECTION BY THE UVRABC PATHWAY: CRYSTAL STRUCTURE TITLE 2 OF UVRB 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 COMPND 9 DINA; COMPND 10 EC: 3.1.-.-; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: UVRABC SYSTEM PROTEIN B; COMPND 14 CHAIN: B; COMPND 15 FRAGMENT: RESIDUES 622-659; COMPND 16 SYNONYM: PROTEIN UVRB, EXCINUCLEASE ABC SUBUNIT B, PROTEIN COMPND 17 DINA; COMPND 18 EC: 3.1.-.-; COMPND 19 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 KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.R.WATERS,J.ERYILMAZ,S.GEDDES,T.E.BARRETT 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 JRNL TITL 2 STRUCTURE OF 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 1 REMARK 2 REMARK 2 RESOLUTION. 2.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2317 ; 1.799 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2051 ; 3.052 ; 4.500 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 REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 2NMV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-OCT-06. REMARK 100 THE RCSB ID CODE IS RCSB040055. 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 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 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. = 3.6 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 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 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 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 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NML D 103 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 REMARK 900 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 ADP A 662 27 HET NML D 103 5 HET FLU D 600 16 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM NML N-METHYLACETAMIDE HETNAM FLU 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID HETSYN FLU FLUORESCEIN FORMUL 4 ADP C10 H15 N5 O10 P2 FORMUL 5 NML C3 H7 N O FORMUL 6 FLU C20 H12 O5 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