PDB Short entry for 2WOC HEADER HYDROLASE 23-JUL-09 2WOC TITLE CRYSTAL STRUCTURE OF THE DINITROGENASE REDUCTASE-ACTIVATING TITLE 2 GLYCOHYDROLASE (DRAG) FROM RHODOSPIRILLUM RUBRUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: ADP-RIBOSYLGLYCOHYDROLASE, DINITROGENASE COMPND 5 REDUCTASE-ACTIVATING GLYCOHYDROLASE; COMPND 6 EC: 3.2.2.24; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOSPIRILLUM RUBRUM; SOURCE 3 ORGANISM_TAXID: 1085; SOURCE 4 STRAIN: S1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 STAR(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-2 KEYWDS HYDROLASE, DIMANGANESE, NITROGEN FIXATION, KEYWDS 2 ADP-RIBOSYLGLYCOHYDROLASE, MONO-ADP-RIBOSYLHYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.L.BERTHOLD,H.WANG,S.NORDLUND,M.HOGBOM REVDAT 3 13-JUL-11 2WOC 1 VERSN REVDAT 2 08-SEP-09 2WOC 1 JRNL REVDAT 1 11-AUG-09 2WOC 0 JRNL AUTH C.L.BERTHOLD,H.WANG,S.NORDLUND,M.HOGBOM JRNL TITL MECHANISM OF ADP-RIBOSYLATION REMOVAL REVEALED BY THE JRNL TITL 2 STRUCTURE AND LIGAND COMPLEXES OF THE DIMANGANESE JRNL TITL 3 MONO-ADP-RIBOSYLHYDROLASE DRAG. JRNL REF PROC.NATL.ACAD.SCI.USA V. 106 14247 2009 JRNL REFN ISSN 0027-8424 JRNL PMID 19706507 JRNL DOI 10.1073/PNAS.0905906106 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 89.79 REMARK 3 NUMBER OF REFLECTIONS : 33434 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) : 0.17757 REMARK 3 R VALUE (WORKING SET) : 0.17425 REMARK 3 FREE R VALUE : 0.24016 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 1780 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) : 2.200 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.257 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1501 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 53.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.221 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.296 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6626 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 372 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 25.3 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.495 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.64 REMARK 3 B22 (A**2) : 0.32 REMARK 3 B33 (A**2) : -0.85 REMARK 3 B12 (A**2) : -1.75 REMARK 3 B13 (A**2) : 0.53 REMARK 3 B23 (A**2) : 0.26 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.469 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.256 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.172 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.035 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.904 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6796 ; 0.008 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9192 ; 1.113 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 878 ; 4.784 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 293 ;34.870 ;22.799 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1112 ;17.085 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 59 ;16.580 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1018 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5150 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3524 ; 0.189 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4702 ; 0.293 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 340 ; 0.147 ; 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): 121 ; 0.255 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 32 ; 0.198 ; 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): 4421 ; 0.267 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6834 ; 0.498 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2679 ; 1.135 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2354 ; 1.855 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B C REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 3 A 293 3 REMARK 3 1 B 3 B 293 3 REMARK 3 1 C 3 C 293 3 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 1160 ; 0.04 ; 0.05 REMARK 3 TIGHT POSITIONAL 1 B (A): 1160 ; 0.04 ; 0.05 REMARK 3 TIGHT POSITIONAL 1 C (A): 1160 ; 0.04 ; 0.05 REMARK 3 LOOSE POSITIONAL 1 A (A): 1022 ; 0.66 ; 5.00 REMARK 3 LOOSE POSITIONAL 1 B (A): 1022 ; 0.68 ; 5.00 REMARK 3 LOOSE POSITIONAL 1 C (A): 1022 ; 0.78 ; 5.00 REMARK 3 TIGHT THERMAL 1 A (A**2): 1160 ; 0.06 ; 0.50 REMARK 3 TIGHT THERMAL 1 B (A**2): 1160 ; 0.07 ; 0.50 REMARK 3 TIGHT THERMAL 1 C (A**2): 1160 ; 0.06 ; 0.50 REMARK 3 LOOSE THERMAL 1 A (A**2): 1022 ; 1.08 ; 10.00 REMARK 3 LOOSE THERMAL 1 B (A**2): 1022 ; 1.27 ; 10.00 REMARK 3 LOOSE THERMAL 1 C (A**2): 1022 ; 1.14 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3 A 293 REMARK 3 ORIGIN FOR THE GROUP (A): 2.9016 45.9927 0.3901 REMARK 3 T TENSOR REMARK 3 T11: -0.1263 T22: -0.1316 REMARK 3 T33: -0.1532 T12: -0.0032 REMARK 3 T13: -0.0098 T23: 0.0103 REMARK 3 L TENSOR REMARK 3 L11: 1.4659 L22: 1.8443 REMARK 3 L33: 1.5576 L12: -0.1630 REMARK 3 L13: -0.5551 L23: -0.2293 REMARK 3 S TENSOR REMARK 3 S11: 0.0193 S12: 0.0420 S13: 0.0607 REMARK 3 S21: 0.0798 S22: -0.0085 S23: 0.0548 REMARK 3 S31: -0.0570 S32: -0.0452 S33: -0.0107 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 293 REMARK 3 ORIGIN FOR THE GROUP (A): -8.1652 26.7728 30.1459 REMARK 3 T TENSOR REMARK 3 T11: -0.0716 T22: -0.1303 REMARK 3 T33: -0.1793 T12: 0.0023 REMARK 3 T13: -0.0022 T23: 0.0141 REMARK 3 L TENSOR REMARK 3 L11: 1.2331 L22: 3.4817 REMARK 3 L33: 1.2424 L12: 0.7229 REMARK 3 L13: -0.1330 L23: 0.2967 REMARK 3 S TENSOR REMARK 3 S11: -0.0448 S12: 0.0063 S13: 0.0233 REMARK 3 S21: -0.2317 S22: -0.0030 S23: 0.1253 REMARK 3 S31: -0.0326 S32: -0.0581 S33: 0.0479 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 3 C 293 REMARK 3 ORIGIN FOR THE GROUP (A): 14.0946 56.0895 58.4549 REMARK 3 T TENSOR REMARK 3 T11: -0.1220 T22: -0.0820 REMARK 3 T33: -0.1058 T12: -0.0044 REMARK 3 T13: 0.0068 T23: 0.0119 REMARK 3 L TENSOR REMARK 3 L11: 2.3996 L22: 2.0366 REMARK 3 L33: 2.5018 L12: 1.2595 REMARK 3 L13: 0.0599 L23: 0.2714 REMARK 3 S TENSOR REMARK 3 S11: -0.0506 S12: -0.0079 S13: 0.2278 REMARK 3 S21: -0.1528 S22: 0.0174 S23: 0.0952 REMARK 3 S31: -0.0655 S32: -0.0632 S33: 0.0332 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 2WOC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JUL-09. REMARK 100 THE PDBE ID CODE IS EBI-40047. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.127 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35220 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.20 REMARK 200 RESOLUTION RANGE LOW (A) : 94.07 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.8 REMARK 200 DATA REDUNDANCY : 3.9 REMARK 200 R MERGE (I) : 0.11 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.00 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.8 REMARK 200 R MERGE FOR SHELL (I) : 0.47 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.50 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: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 GLY A -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 ASP A 294 REMARK 465 GLY B -4 REMARK 465 PRO B -3 REMARK 465 LEU B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 ASP B 294 REMARK 465 GLY C -4 REMARK 465 PRO C -3 REMARK 465 LEU C -2 REMARK 465 GLY C -1 REMARK 465 SER C 0 REMARK 465 MET C 1 REMARK 465 THR C 2 REMARK 465 ASP C 294 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 THR A 59 -149.58 -128.44 REMARK 500 ARG A 94 76.80 61.46 REMARK 500 ALA A 124 32.65 -91.03 REMARK 500 SER A 209 26.65 -140.04 REMARK 500 THR B 59 -150.27 -128.95 REMARK 500 ARG B 94 75.34 61.41 REMARK 500 SER B 209 30.05 -141.19 REMARK 500 THR C 59 -148.98 -124.69 REMARK 500 ARG C 94 77.37 62.08 REMARK 500 SER C 209 30.26 -140.43 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 MN A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN C 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN C 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT C 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WOD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DINITROGENASE REMARK 900 REDUCTASE-ACTIVATING GLYCOHYDROLASE (DRAG) FROM REMARK 900 RHODOSPIRILLUM RUBRUM IN COMPLEX WITH ADP- REMARK 900 RIBSOYLLYSINE REMARK 900 RELATED ID: 2WOE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE D97N VARIANT OF REMARK 900 DINITROGENASE REDUCTASE-ACTIVATING GLYCOHYDROLASE REMARK 900 (DRAG) FROM RHODOSPIRILLUM RUBRUM IN COMPLEX REMARK 900 WITH ADP-RIBOSE DBREF 2WOC A -4 0 PDB 2WOC 2WOC -4 0 DBREF 2WOC A 1 294 UNP P14300 DRAG_RHORU 1 294 DBREF 2WOC B -4 0 PDB 2WOC 2WOC -4 0 DBREF 2WOC B 1 294 UNP P14300 DRAG_RHORU 1 294 DBREF 2WOC C -4 0 PDB 2WOC 2WOC -4 0 DBREF 2WOC C 1 294 UNP P14300 DRAG_RHORU 1 294 SEQRES 1 A 299 GLY PRO LEU GLY SER MET THR GLY PRO SER VAL HIS ASP SEQRES 2 A 299 ARG ALA LEU GLY ALA PHE LEU GLY LEU ALA VAL GLY ASP SEQRES 3 A 299 ALA LEU GLY ALA THR VAL GLU PHE MET THR LYS GLY GLU SEQRES 4 A 299 ILE ALA GLN GLN TYR GLY ILE HIS ARG LYS MET THR GLY SEQRES 5 A 299 GLY GLY TRP LEU ARG LEU LYS PRO GLY GLN ILE THR ASP SEQRES 6 A 299 ASP THR GLU MET SER LEU ALA LEU GLY ARG SER LEU ALA SEQRES 7 A 299 ALA LYS GLY THR LEU ASP VAL ALA ASP ILE CYS GLU GLU SEQRES 8 A 299 PHE ALA LEU TRP LEU LYS SER ARG PRO VAL ASP VAL GLY SEQRES 9 A 299 ASN THR CYS ARG ARG GLY ILE ARG ARG TYR MET HIS GLU SEQRES 10 A 299 GLY THR THR THR ALA PRO TYR SER GLU GLY ASP ALA GLY SEQRES 11 A 299 ASN GLY ALA ALA MET ARG CYS LEU PRO ALA ALA LEU ALA SEQRES 12 A 299 THR LEU GLY HIS PRO ALA ASP LEU GLU PRO TRP VAL LEU SEQRES 13 A 299 ALA GLN ALA ARG ILE THR HIS ASN HIS PRO LEU SER ASP SEQRES 14 A 299 ALA ALA CYS LEU THR LEU GLY ARG MET VAL HIS HIS LEU SEQRES 15 A 299 ILE GLY GLY ARG GLY MET LYS ALA CYS ARG GLU GLU ALA SEQRES 16 A 299 ASN ARG LEU VAL HIS GLN HIS ARG ASP PHE HIS PHE GLU SEQRES 17 A 299 PRO TYR LYS GLY GLN SER SER ALA TYR ILE VAL ASP THR SEQRES 18 A 299 MET GLN THR VAL LEU HIS TYR TYR PHE VAL THR ASP THR SEQRES 19 A 299 PHE LYS SER CYS LEU ILE GLN THR VAL ASN GLN GLY GLY SEQRES 20 A 299 ASP ALA ASP THR THR GLY ALA LEU ALA GLY MET LEU ALA SEQRES 21 A 299 GLY ALA THR TYR GLY VAL ASP ASP ILE PRO SER GLY TRP SEQRES 22 A 299 LEU SER LYS LEU ASP MET LYS VAL GLU ARG GLU ILE ARG SEQRES 23 A 299 ARG GLN VAL ASP ALA LEU LEU ALA LEU ALA GLY LEU ASP SEQRES 1 B 299 GLY PRO LEU GLY SER MET THR GLY PRO SER VAL HIS ASP SEQRES 2 B 299 ARG ALA LEU GLY ALA PHE LEU GLY LEU ALA VAL GLY ASP SEQRES 3 B 299 ALA LEU GLY ALA THR VAL GLU PHE MET THR LYS GLY GLU SEQRES 4 B 299 ILE ALA GLN GLN TYR GLY ILE HIS ARG LYS MET THR GLY SEQRES 5 B 299 GLY GLY TRP LEU ARG LEU LYS PRO GLY GLN ILE THR ASP SEQRES 6 B 299 ASP THR GLU MET SER LEU ALA LEU GLY ARG SER LEU ALA SEQRES 7 B 299 ALA LYS GLY THR LEU ASP VAL ALA ASP ILE CYS GLU GLU SEQRES 8 B 299 PHE ALA LEU TRP LEU LYS SER ARG PRO VAL ASP VAL GLY SEQRES 9 B 299 ASN THR CYS ARG ARG GLY ILE ARG ARG TYR MET HIS GLU SEQRES 10 B 299 GLY THR THR THR ALA PRO TYR SER GLU GLY ASP ALA GLY SEQRES 11 B 299 ASN GLY ALA ALA MET ARG CYS LEU PRO ALA ALA LEU ALA SEQRES 12 B 299 THR LEU GLY HIS PRO ALA ASP LEU GLU PRO TRP VAL LEU SEQRES 13 B 299 ALA GLN ALA ARG ILE THR HIS ASN HIS PRO LEU SER ASP SEQRES 14 B 299 ALA ALA CYS LEU THR LEU GLY ARG MET VAL HIS HIS LEU SEQRES 15 B 299 ILE GLY GLY ARG GLY MET LYS ALA CYS ARG GLU GLU ALA SEQRES 16 B 299 ASN ARG LEU VAL HIS GLN HIS ARG ASP PHE HIS PHE GLU SEQRES 17 B 299 PRO TYR LYS GLY GLN SER SER ALA TYR ILE VAL ASP THR SEQRES 18 B 299 MET GLN THR VAL LEU HIS TYR TYR PHE VAL THR ASP THR SEQRES 19 B 299 PHE LYS SER CYS LEU ILE GLN THR VAL ASN GLN GLY GLY SEQRES 20 B 299 ASP ALA ASP THR THR GLY ALA LEU ALA GLY MET LEU ALA SEQRES 21 B 299 GLY ALA THR TYR GLY VAL ASP ASP ILE PRO SER GLY TRP SEQRES 22 B 299 LEU SER LYS LEU ASP MET LYS VAL GLU ARG GLU ILE ARG SEQRES 23 B 299 ARG GLN VAL ASP ALA LEU LEU ALA LEU ALA GLY LEU ASP SEQRES 1 C 299 GLY PRO LEU GLY SER MET THR GLY PRO SER VAL HIS ASP SEQRES 2 C 299 ARG ALA LEU GLY ALA PHE LEU GLY LEU ALA VAL GLY ASP SEQRES 3 C 299 ALA LEU GLY ALA THR VAL GLU PHE MET THR LYS GLY GLU SEQRES 4 C 299 ILE ALA GLN GLN TYR GLY ILE HIS ARG LYS MET THR GLY SEQRES 5 C 299 GLY GLY TRP LEU ARG LEU LYS PRO GLY GLN ILE THR ASP SEQRES 6 C 299 ASP THR GLU MET SER LEU ALA LEU GLY ARG SER LEU ALA SEQRES 7 C 299 ALA LYS GLY THR LEU ASP VAL ALA ASP ILE CYS GLU GLU SEQRES 8 C 299 PHE ALA LEU TRP LEU LYS SER ARG PRO VAL ASP VAL GLY SEQRES 9 C 299 ASN THR CYS ARG ARG GLY ILE ARG ARG TYR MET HIS GLU SEQRES 10 C 299 GLY THR THR THR ALA PRO TYR SER GLU GLY ASP ALA GLY SEQRES 11 C 299 ASN GLY ALA ALA MET ARG CYS LEU PRO ALA ALA LEU ALA SEQRES 12 C 299 THR LEU GLY HIS PRO ALA ASP LEU GLU PRO TRP VAL LEU SEQRES 13 C 299 ALA GLN ALA ARG ILE THR HIS ASN HIS PRO LEU SER ASP SEQRES 14 C 299 ALA ALA CYS LEU THR LEU GLY ARG MET VAL HIS HIS LEU SEQRES 15 C 299 ILE GLY GLY ARG GLY MET LYS ALA CYS ARG GLU GLU ALA SEQRES 16 C 299 ASN ARG LEU VAL HIS GLN HIS ARG ASP PHE HIS PHE GLU SEQRES 17 C 299 PRO TYR LYS GLY GLN SER SER ALA TYR ILE VAL ASP THR SEQRES 18 C 299 MET GLN THR VAL LEU HIS TYR TYR PHE VAL THR ASP THR SEQRES 19 C 299 PHE LYS SER CYS LEU ILE GLN THR VAL ASN GLN GLY GLY SEQRES 20 C 299 ASP ALA ASP THR THR GLY ALA LEU ALA GLY MET LEU ALA SEQRES 21 C 299 GLY ALA THR TYR GLY VAL ASP ASP ILE PRO SER GLY TRP SEQRES 22 C 299 LEU SER LYS LEU ASP MET LYS VAL GLU ARG GLU ILE ARG SEQRES 23 C 299 ARG GLN VAL ASP ALA LEU LEU ALA LEU ALA GLY LEU ASP HET MN A 400 1 HET MN A 401 1 HET FMT A 402 3 HET GOL A 500 6 HET CL A 501 1 HET GOL A 502 6 HET MN B 400 1 HET MN B 401 1 HET FMT B 402 3 HET GOL B 500 6 HET CL B 501 1 HET GOL B 502 6 HET MN C 400 1 HET MN C 401 1 HET FMT C 402 3 HETNAM MN MANGANESE (II) ION HETNAM FMT FORMIC ACID HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION FORMUL 4 MN 6(MN 2+) FORMUL 5 FMT 3(C H2 O2) FORMUL 6 GOL 4(C3 H8 O3) FORMUL 7 CL 2(CL 1-) FORMUL 8 HOH *372(H2 O) HELIX 1 1 SER A 5 LEU A 11 1 7 HELIX 2 2 GLU A 34 TYR A 39 1 6 HELIX 3 3 THR A 59 LEU A 68 1 10 HELIX 4 4 ARG A 70 LYS A 75 1 6 HELIX 5 5 ASP A 79 SER A 93 1 15 HELIX 6 6 ILE A 106 GLU A 112 1 7 HELIX 7 7 ALA A 128 ARG A 131 5 4 HELIX 8 8 CYS A 132 THR A 139 1 8 HELIX 9 9 HIS A 142 ALA A 144 5 3 HELIX 10 10 ASP A 145 ILE A 156 1 12 HELIX 11 11 HIS A 160 LEU A 170 1 11 HELIX 12 12 ARG A 172 ILE A 178 1 7 HELIX 13 13 MET A 183 HIS A 197 1 15 HELIX 14 14 ARG A 198 HIS A 201 5 4 HELIX 15 15 TYR A 212 THR A 227 1 16 HELIX 16 16 THR A 229 ASN A 239 1 11 HELIX 17 17 TRP A 268 LEU A 272 5 5 HELIX 18 18 ASP A 273 ALA A 291 1 19 HELIX 19 19 SER B 5 LEU B 11 1 7 HELIX 20 20 GLU B 34 TYR B 39 1 6 HELIX 21 21 THR B 59 LEU B 68 1 10 HELIX 22 22 ARG B 70 LYS B 75 1 6 HELIX 23 23 ASP B 79 SER B 93 1 15 HELIX 24 24 ILE B 106 GLU B 112 1 7 HELIX 25 25 ALA B 128 ARG B 131 5 4 HELIX 26 26 CYS B 132 THR B 139 1 8 HELIX 27 27 HIS B 142 ALA B 144 5 3 HELIX 28 28 ASP B 145 ARG B 155 1 11 HELIX 29 29 HIS B 160 LEU B 170 1 11 HELIX 30 30 ARG B 172 ILE B 178 1 7 HELIX 31 31 MET B 183 HIS B 197 1 15 HELIX 32 32 ARG B 198 HIS B 201 5 4 HELIX 33 33 TYR B 212 THR B 227 1 16 HELIX 34 34 THR B 229 ASN B 239 1 11 HELIX 35 35 TRP B 268 LEU B 272 5 5 HELIX 36 36 ASP B 273 ALA B 291 1 19 HELIX 37 37 SER C 5 LEU C 11 1 7 HELIX 38 38 GLU C 34 TYR C 39 1 6 HELIX 39 39 THR C 59 LEU C 68 1 10 HELIX 40 40 ARG C 70 LYS C 75 1 6 HELIX 41 41 ASP C 79 SER C 93 1 15 HELIX 42 42 ILE C 106 GLU C 112 1 7 HELIX 43 43 ALA C 128 ARG C 131 5 4 HELIX 44 44 CYS C 132 ALA C 138 1 7 HELIX 45 45 HIS C 142 ALA C 144 5 3 HELIX 46 46 ASP C 145 ILE C 156 1 12 HELIX 47 47 HIS C 160 LEU C 170 1 11 HELIX 48 48 ARG C 172 ILE C 178 1 7 HELIX 49 49 MET C 183 HIS C 197 1 15 HELIX 50 50 ARG C 198 HIS C 201 5 4 HELIX 51 51 TYR C 212 THR C 227 1 16 HELIX 52 52 THR C 229 ASN C 239 1 11 HELIX 53 53 TRP C 268 LEU C 272 5 5 HELIX 54 54 ASP C 273 ALA C 291 1 19 CISPEP 1 GLU A 203 PRO A 204 0 -1.12 CISPEP 2 GLU B 203 PRO B 204 0 -0.68 CISPEP 3 GLU C 203 PRO C 204 0 -3.88 SITE 1 AC1 5 ASP A 243 ASP A 245 THR A 246 FMT A 402 SITE 2 AC1 5 HOH A2012 SITE 1 AC2 5 GLU A 28 THR A 59 ASP A 60 ASP A 97 SITE 2 AC2 5 ASP A 245 SITE 1 AC3 6 ASP A 60 ASN A 126 MET A 130 ASP A 245 SITE 2 AC3 6 THR A 246 MN A 400 SITE 1 AC4 7 SER A 270 LYS A 271 LEU A 272 ASP A 273 SITE 2 AC4 7 MET A 274 HOH A2031 GLN C 208 SITE 1 AC5 1 MET A 45 SITE 1 AC6 7 ARG A 43 LYS A 44 LYS A 231 PRO A 265 SITE 2 AC6 7 GLY A 267 TRP A 268 HOH A2145 SITE 1 AC7 5 ASP B 243 ASP B 245 THR B 246 FMT B 402 SITE 2 AC7 5 HOH B2013 SITE 1 AC8 5 GLU B 28 THR B 59 ASP B 60 ASP B 97 SITE 2 AC8 5 ASP B 245 SITE 1 AC9 7 ASP B 60 ASN B 126 MET B 130 ASP B 243 SITE 2 AC9 7 THR B 246 MN B 400 HOH B2125 SITE 1 BC1 8 ALA B 165 ARG B 172 ARG B 192 LEU B 193 SITE 2 BC1 8 GLN B 196 HIS B 197 HOH B2090 HOH B2126 SITE 1 BC2 3 MET B 45 LYS B 271 GOL B 502 SITE 1 BC3 4 ARG B 43 GLY B 267 TRP B 268 CL B 501 SITE 1 BC4 5 ASP C 243 ASP C 245 THR C 246 FMT C 402 SITE 2 BC4 5 HOH C2101 SITE 1 BC5 5 GLU C 28 THR C 59 ASP C 60 ASP C 97 SITE 2 BC5 5 ASP C 245 SITE 1 BC6 7 ASP C 60 ASN C 126 MET C 130 ASP C 243 SITE 2 BC6 7 ASP C 245 THR C 246 MN C 400 CRYST1 44.771 47.537 95.212 80.84 86.56 85.83 P 1 3 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 0.022336 -0.001628 -0.001103 0.00000 SCALE2 0.000000 0.021092 -0.003321 0.00000 SCALE3 0.000000 0.000000 0.010651 0.00000 MTRIX1 1 -0.408000 0.890000 0.203000 -30.39517 1 MTRIX2 1 -0.880000 -0.323000 -0.349000 57.98450 1 MTRIX3 1 -0.245000 -0.321000 0.915000 -20.58209 1 MTRIX1 2 -0.378000 -0.887000 -0.265000 73.45803 1 MTRIX2 2 0.882000 -0.257000 -0.395000 71.11835 1 MTRIX3 2 0.283000 -0.383000 0.880000 -33.54707 1