PDB Short entry for 2B9S HEADER ISOMERASE/DNA 12-OCT-05 2B9S TITLE CRYSTAL STRUCTURE OF HETERODIMERIC L. DONOVANI TOPOISOMERASE I- TITLE 2 VANADATE-DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3'; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'; COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*AP*AP*GP*TP*CP*TP COMPND 11 *TP*TP*TP*T)-3'; COMPND 12 CHAIN: E; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: TOPOISOMERASE I-LIKE PROTEIN; COMPND 16 CHAIN: A; COMPND 17 EC: 5.99.1.2; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 5; COMPND 20 MOLECULE: DNA TOPOISOMERASE I-LIKE PROTEIN; COMPND 21 CHAIN: B; COMPND 22 EC: 5.99.1.2; COMPND 23 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES; SOURCE 7 MOL_ID: 4; SOURCE 8 ORGANISM_SCIENTIFIC: LEISHMANIA DONOVANI; SOURCE 9 ORGANISM_TAXID: 5661; SOURCE 10 GENE: TOPOISOMERASE I, LARGE SUBUNIT (LDTOP1L); SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PLYSS; SOURCE 16 MOL_ID: 5; SOURCE 17 ORGANISM_SCIENTIFIC: LEISHMANIA DONOVANI; SOURCE 18 ORGANISM_TAXID: 5661; SOURCE 19 GENE: TOPOISOMERASE I, SMALL SUBUNIT (LDTOP1S); SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 21 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 22 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 23 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 24 EXPRESSION_SYSTEM_PLASMID: PLYSS KEYWDS TOPOISOMERASE I, VANADATE COMPLEX, ISOMERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.R.DAVIES,W.G.J.HOL REVDAT 5 14-FEB-24 2B9S 1 REMARK REVDAT 4 11-OCT-17 2B9S 1 REMARK REVDAT 3 24-FEB-09 2B9S 1 VERSN REVDAT 2 04-APR-06 2B9S 1 JRNL REVDAT 1 17-JAN-06 2B9S 0 JRNL AUTH D.R.DAVIES,A.MUSHTAQ,H.INTERTHAL,J.J.CHAMPOUX,W.G.HOL JRNL TITL THE STRUCTURE OF THE TRANSITION STATE OF THE HETERODIMERIC JRNL TITL 2 TOPOISOMERASE I OF LEISHMANIA DONOVANI AS A VANADATE COMPLEX JRNL TITL 3 WITH NICKED DNA. JRNL REF J.MOL.BIOL. V. 357 1202 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16487540 JRNL DOI 10.1016/J.JMB.2006.01.022 REMARK 2 REMARK 2 RESOLUTION. 2.27 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) : 2.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 43746 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) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2217 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) : 2.27 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2131 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3370 REMARK 3 BIN FREE R VALUE SET COUNT : 126 REMARK 3 BIN FREE R VALUE : 0.3990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3715 REMARK 3 NUCLEIC ACID ATOMS : 889 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.57000 REMARK 3 B22 (A**2) : 0.50000 REMARK 3 B33 (A**2) : 1.07000 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): 0.245 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.215 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.159 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.412 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4813 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6725 ; 1.597 ; 2.172 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 475 ; 5.977 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 176 ;34.726 ;23.523 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 577 ;15.234 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;16.015 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 734 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3414 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1869 ; 0.191 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3121 ; 0.301 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 213 ; 0.143 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.185 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 29 ; 0.194 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 1 ; 0.352 ; 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): 2452 ; 1.491 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3810 ; 2.320 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2957 ; 1.851 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2915 ; 2.788 ; 4.000 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: NULL REMARK 4 REMARK 4 2B9S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1000034853. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43803 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.270 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.07300 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) : 2.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.40800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 3350, 0.2 M NA2HPO4, 0.1 M REMARK 280 LICL, PH 9.1, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 36.21650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.34550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.05100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.34550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.21650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.05100 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 IS A HETERODIMER CONSISTING OF ONE REMARK 300 COPY EACH OF THE LARGE AND SMALL SUBUNITS AND A DNA DUPLEX. 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: PENTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, E, 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 GLU A 25 REMARK 465 GLU A 26 REMARK 465 VAL A 427 REMARK 465 ASP A 428 REMARK 465 PRO A 429 REMARK 465 LYS A 430 REMARK 465 GLU B 201 REMARK 465 ASN B 202 REMARK 465 ILE B 203 REMARK 465 ILE B 204 REMARK 465 ARG B 205 REMARK 465 ILE B 206 REMARK 465 LYS B 207 REMARK 465 ASP B 208 REMARK 465 ASP B 209 REMARK 465 ASN B 210 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 E 107 C7 REMARK 470 DT E 108 C7 REMARK 470 DT E 109 C7 REMARK 470 DT E 110 C7 REMARK 470 ASP A 27 CG OD1 OD2 REMARK 470 GLU A 34 CG CD OE1 OE2 REMARK 470 ASN A 35 CG OD1 ND2 REMARK 470 ARG A 37 CG CD NE CZ NH1 NH2 REMARK 470 MET A 40 CG SD CE REMARK 470 GLU A 59 CG CD OE1 OE2 REMARK 470 GLU A 61 CG CD OE1 OE2 REMARK 470 ARG A 72 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 92 CG CD OE1 OE2 REMARK 470 ARG A 97 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 107 CG CD OE1 OE2 REMARK 470 GLN A 117 CG CD OE1 NE2 REMARK 470 ARG A 121 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 122 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 124 CG CD OE1 OE2 REMARK 470 ARG A 139 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 140 CG CD OE1 OE2 REMARK 470 LYS A 141 CG CD CE NZ REMARK 470 ARG A 145 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 147 CG CD CE NZ REMARK 470 GLU A 148 CG CD OE1 OE2 REMARK 470 GLU A 149 CG CD OE1 OE2 REMARK 470 LYS A 150 CG CD CE NZ REMARK 470 LYS A 151 CG CD CE NZ REMARK 470 ILE A 153 CG1 CG2 CD1 REMARK 470 LYS A 154 CG CD CE NZ REMARK 470 GLU A 155 CG CD OE1 OE2 REMARK 470 LYS A 156 CG CD CE NZ REMARK 470 GLN A 157 CG CD OE1 NE2 REMARK 470 ARG A 165 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 172 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 192 CG CD CE NZ REMARK 470 LYS A 275 CG CD CE NZ REMARK 470 LYS A 279 CG CD CE NZ REMARK 470 GLU A 289 CG CD OE1 OE2 REMARK 470 LYS A 292 CG CD CE NZ REMARK 470 GLU A 321 CG CD OE1 OE2 REMARK 470 GLU A 366 CG CD OE1 OE2 REMARK 470 ARG A 377 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 420 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 425 CG CD CE NZ REMARK 470 THR A 433 OG1 CG2 REMARK 470 LYS A 436 CG CD CE NZ REMARK 470 LYS A 442 CG CD CE NZ REMARK 470 LYS A 455 CG CD CE NZ REMARK 470 LYS B 219 CG CD CE NZ REMARK 470 LYS B 233 CG CD CE NZ REMARK 470 GLN B 235 CG CD OE1 NE2 REMARK 470 ASP B 236 CG OD1 OD2 REMARK 470 ILE B 239 CG1 CG2 CD1 REMARK 470 ASN B 240 CG OD1 ND2 REMARK 470 LYS B 241 CG CD CE NZ REMARK 470 LYS B 249 CG CD CE NZ REMARK 470 ASN B 256 CG OD1 ND2 REMARK 470 GLU B 258 CG CD OE1 OE2 REMARK 470 ASN B 259 CG OD1 ND2 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 DA C 5 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 DC C 8 O5' - P - OP1 ANGL. DEV. = 7.5 DEGREES REMARK 500 DC C 8 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DC C 8 C1' - O4' - C4' ANGL. DEV. = -7.9 DEGREES REMARK 500 DC C 8 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES REMARK 500 DC C 8 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA D 13 O4' - C1' - N9 ANGL. DEV. = -5.0 DEGREES REMARK 500 DA D 13 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DA D 16 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DA E 102 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT E 112 C3' - C2' - C1' ANGL. DEV. = -7.0 DEGREES REMARK 500 DT E 112 O4' - C1' - N1 ANGL. DEV. = 7.8 DEGREES REMARK 500 DA E 114 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT E 116 C4 - C5 - C7 ANGL. DEV. = 4.5 DEGREES REMARK 500 DC E 117 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT E 119 C4 - C5 - C7 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT E 119 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 DT E 120 C4 - C5 - C7 ANGL. DEV. = 3.6 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 GLU A 34 -74.86 -63.74 REMARK 500 ASN A 178 55.36 -114.22 REMARK 500 ASP A 342 63.01 -101.41 REMARK 500 PHE A 385 60.23 -100.53 REMARK 500 ILE B 242 -51.11 -126.38 REMARK 500 ALA B 257 78.38 46.02 REMARK 500 ASN B 259 53.46 38.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN B 256 ALA B 257 131.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 VO4 B 301 V REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT C 10 O3' REMARK 620 2 VO4 B 301 O1 120.1 REMARK 620 3 VO4 B 301 O2 117.7 122.1 REMARK 620 4 DA D 11 O5' 85.3 91.4 96.7 REMARK 620 5 TYR B 222 OH 91.6 95.5 79.4 173.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VO4 B 301 DBREF 2B9S A 25 456 GB 5305782 AAD41814 25 456 DBREF 2B9S B 201 262 GB 17528932 AAL38667 201 262 DBREF 2B9S C 1 10 PDB 2B9S 2B9S 1 10 DBREF 2B9S D 11 22 PDB 2B9S 2B9S 11 22 DBREF 2B9S E 101 122 PDB 2B9S 2B9S 101 122 SEQRES 1 C 10 DA DA DA DA DA DG DA DC DT DT SEQRES 1 D 12 DA DG DA DA DA DA DA DT DT DT DT DT SEQRES 1 E 22 DA DA DA DA DA DT DT DT DT DT DC DT DA SEQRES 2 E 22 DA DG DT DC DT DT DT DT DT SEQRES 1 A 432 GLU GLU ASP LEU ASN TRP TRP GLU GLN GLU ASN LEU ARG SEQRES 2 A 432 ILE ALA MET LYS GLY GLU ARG ARG TRP GLU THR LEU ALA SEQRES 3 A 432 HIS ASN GLY VAL LEU PHE PRO PRO GLU TYR GLU PRO HIS SEQRES 4 A 432 GLY ILE PRO ILE PHE TYR ASP GLY ARG GLU PHE LYS MET SEQRES 5 A 432 THR PRO GLU GLU GLU GLU VAL ALA THR MET PHE ALA VAL SEQRES 6 A 432 MET LYS GLU HIS ASP TYR TYR ARG MET GLU VAL PHE ARG SEQRES 7 A 432 ARG ASN PHE PHE GLU SER TRP ARG GLU ILE LEU ASP LYS SEQRES 8 A 432 ARG GLN HIS PRO ILE ARG ARG LEU GLU LEU CYS ASP PHE SEQRES 9 A 432 GLU PRO ILE TYR GLN TRP HIS LEU VAL GLN ARG GLU LYS SEQRES 10 A 432 LYS LEU SER ARG THR LYS GLU GLU LYS LYS ALA ILE LYS SEQRES 11 A 432 GLU LYS GLN ASP ALA GLU ALA GLU PRO TYR ARG TYR CYS SEQRES 12 A 432 VAL TRP ASP GLY ARG ARG GLU GLN VAL ALA ASN PHE ARG SEQRES 13 A 432 VAL GLU PRO PRO GLY LEU PHE ARG GLY ARG GLY LYS HIS SEQRES 14 A 432 PRO LEU MET GLY LYS LEU LYS VAL ARG VAL GLN PRO GLU SEQRES 15 A 432 ASP ILE THR ILE ASN ILE GLY GLU THR ALA GLU VAL PRO SEQRES 16 A 432 VAL PRO PRO ALA GLY HIS LYS TRP ALA ALA VAL GLN HIS SEQRES 17 A 432 ASP HIS THR VAL THR TRP LEU ALA MET TRP ARG ASP SER SEQRES 18 A 432 VAL ALA GLY ASN MET LYS TYR VAL MET LEU ALA PRO SER SEQRES 19 A 432 SER SER VAL LYS GLY GLN SER ASP MET VAL LYS PHE GLU SEQRES 20 A 432 LYS ALA ARG LYS LEU LYS ASP LYS VAL ASP ASP ILE ARG SEQRES 21 A 432 ALA SER TYR MET GLU ASP PHE LYS SER ASN ASP LEU HIS SEQRES 22 A 432 VAL ALA GLN ARG ALA VAL ALA MET TYR PHE ILE ASP ARG SEQRES 23 A 432 LEU ALA LEU ARG VAL GLY ASN GLU LYS GLY GLU ASP GLU SEQRES 24 A 432 ALA ASP THR VAL GLY CYS CYS SER LEU ARG VAL GLU HIS SEQRES 25 A 432 ILE GLN LEU MET PRO ASP ASN ILE VAL ARG PHE ASP PHE SEQRES 26 A 432 LEU GLY LYS ASP SER ILE ARG TYR GLN ASN ASP VAL ALA SEQRES 27 A 432 VAL LEU PRO GLU VAL TYR ALA LEU LEU GLN ARG PHE THR SEQRES 28 A 432 ARG ARG LYS SER PRO GLY MET ASP ILE PHE ASP GLN LEU SEQRES 29 A 432 ASN PRO THR GLN LEU ASN ASP HIS LEU LYS SER PHE MET SEQRES 30 A 432 ASP GLY LEU SER ALA LYS VAL PHE ARG THR TYR ASN ALA SEQRES 31 A 432 SER ILE THR LEU ASP ARG TRP PHE LYS GLU LYS PRO VAL SEQRES 32 A 432 ASP PRO LYS TRP SER THR ALA ASP LYS LEU ALA TYR PHE SEQRES 33 A 432 ASN LYS ALA ASN THR GLU VAL ALA ILE LEU CYS ASN HIS SEQRES 34 A 432 GLN LYS SER SEQRES 1 B 62 GLU ASN ILE ILE ARG ILE LYS ASP ASP ASN LYS ALA VAL SEQRES 2 B 62 SER LEU GLY THR SER LYS ILE ASN TYR ILE ASP PRO ARG SEQRES 3 B 62 ILE ILE CYS SER TRP ALA LYS ALA GLN ASP VAL PRO ILE SEQRES 4 B 62 ASN LYS ILE PHE SER ALA THR ILE GLN LYS LYS PHE PRO SEQRES 5 B 62 TRP ALA MET ASN ALA GLU ASN PHE ASP PHE HET VO4 B 301 3 HETNAM VO4 VANADATE ION FORMUL 6 VO4 O4 V 3- FORMUL 7 HOH *130(H2 O) HELIX 1 1 THR A 77 VAL A 89 1 13 HELIX 2 2 HIS A 93 ARG A 97 5 5 HELIX 3 3 MET A 98 ASP A 114 1 17 HELIX 4 4 ARG A 122 GLU A 124 5 3 HELIX 5 5 PHE A 128 SER A 144 1 17 HELIX 6 6 GLU A 148 GLU A 162 1 15 HELIX 7 7 GLN A 204 ASP A 207 5 4 HELIX 8 8 SER A 259 PHE A 291 1 33 HELIX 9 9 ASP A 295 ALA A 312 1 18 HELIX 10 10 GLY A 328 LEU A 332 5 5 HELIX 11 11 ARG A 333 GLU A 335 5 3 HELIX 12 12 LYS A 352 SER A 354 5 3 HELIX 13 13 LEU A 364 ARG A 376 1 13 HELIX 14 14 ASN A 389 LYS A 398 1 10 HELIX 15 15 LYS A 407 LYS A 425 1 19 HELIX 16 16 ALA A 434 ASN A 452 1 19 HELIX 17 17 LEU B 215 TYR B 222 1 8 HELIX 18 18 ASP B 224 GLN B 235 1 12 HELIX 19 19 PRO B 238 ILE B 242 5 5 HELIX 20 20 SER B 244 PHE B 251 1 8 HELIX 21 21 PRO B 252 MET B 255 5 4 SHEET 1 A 3 LEU A 49 ALA A 50 0 SHEET 2 A 3 TYR A 166 TRP A 169 -1 O VAL A 168 N ALA A 50 SHEET 3 A 3 ARG A 172 GLN A 175 -1 O ARG A 172 N TRP A 169 SHEET 1 B 3 ARG A 72 PHE A 74 0 SHEET 2 B 3 ILE A 67 TYR A 69 -1 N ILE A 67 O PHE A 74 SHEET 3 B 3 CYS A 126 ASP A 127 -1 O ASP A 127 N PHE A 68 SHEET 1 C 2 GLY A 185 LEU A 186 0 SHEET 2 C 2 LEU A 199 LYS A 200 -1 O LYS A 200 N GLY A 185 SHEET 1 D 4 ALA A 229 GLN A 231 0 SHEET 2 D 4 THR A 209 ASN A 211 1 N ILE A 210 O GLN A 231 SHEET 3 D 4 ALA A 240 ARG A 243 -1 O MET A 241 N THR A 209 SHEET 4 D 4 MET A 250 VAL A 253 -1 O LYS A 251 N TRP A 242 SHEET 1 E 3 ILE A 337 LEU A 339 0 SHEET 2 E 3 ILE A 344 LEU A 350 -1 O ARG A 346 N GLN A 338 SHEET 3 E 3 ARG A 356 ALA A 362 -1 O VAL A 361 N VAL A 345 SHEET 1 F 2 GLN A 454 LYS A 455 0 SHEET 2 F 2 ALA B 212 VAL B 213 -1 O ALA B 212 N LYS A 455 LINK O3' DT C 10 V VO4 B 301 1555 1555 1.78 LINK O5' DA D 11 V VO4 B 301 1555 1555 2.01 LINK OH TYR B 222 V VO4 B 301 1555 1555 2.11 SITE 1 AC1 7 ARG A 314 ARG A 410 HIS A 453 TYR B 222 SITE 2 AC1 7 HOH B 303 DT C 10 DA D 11 CRYST1 72.433 106.102 126.691 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 0.013810 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009430 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007890 0.00000