HEADER HYDROLASE/DNA 18-NOV-05 2D7D TITLE STRUCTURAL INSIGHTS INTO THE CRYPTIC DNA DEPENDENT ATP-ASE ACTIVITY OF TITLE 2 UVRB COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(P*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: UVRB PROTEIN, EXCINUCLEASE ABC SUBUNIT B, PROTEIN DINA; COMPND 9 EC: 3.1.-.-; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 40-MER FROM UVRABC SYSTEM PROTEIN B; COMPND 13 CHAIN: B; COMPND 14 EC: 3.1.-.-; COMPND 15 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: BL21 DE3 PLYSS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET 8C; 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: BL21 DE3 PLYSS; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET 8C KEYWDS HELICASE, PROTEIN-DNA-ADP TERNARY COMPLEX, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.E.BARRETT REVDAT 3 25-OCT-23 2D7D 1 REMARK REVDAT 2 24-FEB-09 2D7D 1 VERSN REVDAT 1 02-MAY-06 2D7D 0 JRNL AUTH J.ERYILMAZ,S.CESCHINI,J.RYAN,S.GEDDES,T.R.WATERS,T.E.BARRETT JRNL TITL STRUCTURAL INSIGHTS INTO THE CRYPTIC DNA-DEPENDENT ATPASE JRNL TITL 2 ACTIVITY OF UVRB JRNL REF J.MOL.BIOL. V. 357 62 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16426634 JRNL DOI 10.1016/J.JMB.2005.12.059 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.ERYILMAZ,S.CESCHINI,J.RYAN,S.GEDDES,T.R.WATERS,T.E.BARRETT REMARK 1 TITL STRUCTURAL INSIGHTS INTO THE CRYPTIC ATP-ASE ACTIVITY OF REMARK 1 TITL 2 UVRB REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 39593 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) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1953 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2633 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE SET COUNT : 121 REMARK 3 BIN FREE R VALUE : 0.3460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5199 REMARK 3 NUCLEIC ACID ATOMS : 61 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 204 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.03000 REMARK 3 B22 (A**2) : -0.85000 REMARK 3 B33 (A**2) : -1.18000 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): 0.292 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.236 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.186 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.237 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.925 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.884 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5377 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7283 ; 1.610 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 656 ; 6.340 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 262 ;35.976 ;24.046 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 945 ;18.419 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 47 ;19.562 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 826 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4044 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2437 ; 0.219 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3656 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 280 ; 0.178 ; 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): 91 ; 0.273 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 23 ; 0.321 ; 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): 3384 ; 0.780 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5278 ; 1.273 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2220 ; 2.210 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2005 ; 3.396 ; 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 2D7D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1000025078. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-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 : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL-CUT MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39593 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.400 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : 0.08200 REMARK 200 FOR THE DATA SET : 5.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.31000 REMARK 200 R SYM FOR SHELL (I) : 0.31000 REMARK 200 FOR SHELL : 2.400 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 1D9X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18-20% (W/V) PEG 10000 0.1M TRIS-HCL, REMARK 280 PH 8.5, 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 37.11550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.70250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.10750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.70250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.11550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.10750 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 300 REMARK: THE BIOLOGICAL ASSEMBLY CONSISTS OF A FULL UVRB MONOMER, A REMARK 300 TRITHYMINE OLIGONUCLEOTIDE, A SINGLE MOLECULE OF ADP AND A HELIX- REMARK 300 LOOP-HELIX DIMER FRAGMENT RESULTING FROM PROTEOLYSIS OF UVRB. 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 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 465 GLU B 660 REMARK 465 GLY B 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 ARG A 4 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 104 CG CD OE1 NE2 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: 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 CG LYS A 265 O HOH A 803 2.16 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 O HOH A 806 O HOH A 817 3555 1.98 REMARK 500 O HOH A 722 O HOH A 757 3455 2.11 REMARK 500 O HOH A 699 O HOH A 842 1655 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 1 P DT D 1 OP3 -0.122 REMARK 500 DT D 3 O3' DT D 3 C3' 0.117 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' - C4' - C3' ANGL. DEV. = -5.8 DEGREES REMARK 500 DT D 1 C1' - O4' - C4' ANGL. DEV. = -6.5 DEGREES REMARK 500 DT D 3 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 LEU A 281 CA - CB - CG ANGL. DEV. = 14.3 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 ALA A 113 146.71 -176.81 REMARK 500 ILE A 167 138.28 166.21 REMARK 500 GLN A 180 17.15 86.81 REMARK 500 GLU A 209 -40.56 -137.50 REMARK 500 ASP A 219 56.64 -91.01 REMARK 500 HIS A 387 -63.61 -101.18 REMARK 500 SER A 393 141.43 -170.86 REMARK 500 GLU A 525 -126.21 47.98 REMARK 500 REMARK 500 REMARK: NULL 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 DBREF 2D7D A 1 661 UNP P37954 UVRB_BACSU 1 661 DBREF 2D7D B 622 661 UNP P37954 UVRB_BACSU 622 661 DBREF 2D7D D 1 3 PDB 2D7D 2D7D 1 3 SEQRES 1 D 3 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 40 LYS GLU ARG GLN LYS VAL VAL GLU GLN MET GLU HIS GLU SEQRES 2 B 40 MET LYS GLU ALA ALA LYS ALA LEU ASP PHE GLU ARG ALA SEQRES 3 B 40 ALA GLU LEU ARG ASP LEU LEU LEU GLU LEU LYS ALA GLU SEQRES 4 B 40 GLY HET ADP A 662 27 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 4 ADP C10 H15 N5 O10 P2 FORMUL 5 HOH *204(H2 O) 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 ILE A 179 1 12 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 5 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 HIS A 385 1 8 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 LEU A 493 1 14 HELIX 20 20 SER A 530 ARG A 540 1 11 HELIX 21 21 THR A 557 GLY A 582 1 26 HELIX 22 22 LYS A 621 ALA A 641 1 21 HELIX 23 23 ASP A 643 LEU A 654 1 12 HELIX 24 24 LYS B 622 ALA B 641 1 20 HELIX 25 25 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 137 N GLU A 87 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 MET A 334 N LEU A 61 SHEET 5 A 7 ASN A 388 VAL A 392 1 O VAL A 392 N VAL A 337 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 VAL A 102 0 SHEET 2 C 2 THR A 107 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 PHE A 203 -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 ASP A 237 -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 VAL A 549 N LEU A 421 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 SITE 1 AC1 15 TYR A 11 GLN A 12 GLN A 14 GLN A 17 SITE 2 AC1 15 THR A 41 GLY A 42 THR A 43 GLY A 44 SITE 3 AC1 15 LYS A 45 PHE A 47 PRO A 414 ARG A 543 SITE 4 AC1 15 HOH A 702 HOH A 728 HOH A 762 CRYST1 74.231 98.215 95.405 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 0.013471 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010182 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010482 0.00000