HEADER HYDROLASE 23-JUL-09 2WOD TITLE CRYSTAL STRUCTURE OF THE DINITROGENASE REDUCTASE-ACTIVATING TITLE 2 GLYCOHYDROLASE (DRAG) FROM RHODOSPIRILLUM RUBRUM IN COMPLEX WITH ADP- TITLE 3 RIBSOYLLYSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DINITROGENASE REDUCTASE-ACTIVATING GLYCOHYDROLASE, ADP- COMPND 5 RIBOSYLGLYCOHYDROLASE; COMPND 6 EC: 3.2.2.24; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: LYS B54 IS MONO-ADP-RIBOSYLATED 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(DE3) STAR; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-2 KEYWDS HYDROLASE, NITROGEN FIXATION, DIMANGANESE-DEPENDENT, ADP- KEYWDS 2 RIBOSYLGLYCOHYDROLASE, MONO-ADP-RIBOSYLHYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.L.BERTHOLD,H.WANG,S.NORDLUND,M.HOGBOM REVDAT 4 17-JAN-18 2WOD 1 REMARK REVDAT 3 13-JUL-11 2WOD 1 VERSN REVDAT 2 08-SEP-09 2WOD 1 JRNL REVDAT 1 11-AUG-09 2WOD 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. 2.25 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 38837 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2082 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2831 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.23 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 139 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4408 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 85 REMARK 3 SOLVENT ATOMS : 249 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 36.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.36000 REMARK 3 B22 (A**2) : 3.36000 REMARK 3 B33 (A**2) : -5.04000 REMARK 3 B12 (A**2) : 1.68000 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): 0.222 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.195 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.169 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.081 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4596 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3071 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6231 ; 1.183 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7449 ; 1.552 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 584 ; 5.147 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 195 ;33.911 ;22.872 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 740 ;15.920 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;17.376 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 690 ; 0.059 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5146 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 944 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1136 ; 0.197 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3286 ; 0.179 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2282 ; 0.170 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2252 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 219 ; 0.132 ; 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): 10 ; 0.148 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 31 ; 0.197 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.097 ; 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): 3728 ; 0.470 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1210 ; 0.076 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4552 ; 0.569 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1985 ; 1.102 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1677 ; 1.659 ; 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 : 2 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): 36.2581 -24.4663 -25.0573 REMARK 3 T TENSOR REMARK 3 T11: 0.1543 T22: -0.2495 REMARK 3 T33: -0.1090 T12: 0.0311 REMARK 3 T13: 0.0449 T23: 0.0191 REMARK 3 L TENSOR REMARK 3 L11: 1.0780 L22: 2.3571 REMARK 3 L33: 4.4203 L12: 0.4351 REMARK 3 L13: -0.4260 L23: -0.5324 REMARK 3 S TENSOR REMARK 3 S11: -0.0400 S12: -0.0713 S13: -0.2535 REMARK 3 S21: -0.2434 S22: -0.0529 S23: -0.2433 REMARK 3 S31: 0.5458 S32: 0.1084 S33: 0.0929 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): 42.2815 10.6576 -13.9611 REMARK 3 T TENSOR REMARK 3 T11: -0.1326 T22: -0.2167 REMARK 3 T33: -0.1722 T12: -0.0309 REMARK 3 T13: -0.0094 T23: -0.0134 REMARK 3 L TENSOR REMARK 3 L11: 1.4156 L22: 2.0624 REMARK 3 L33: 3.4575 L12: 0.7028 REMARK 3 L13: 0.4342 L23: 0.1170 REMARK 3 S TENSOR REMARK 3 S11: -0.0088 S12: -0.1520 S13: 0.0199 REMARK 3 S21: -0.1467 S22: -0.0557 S23: -0.0066 REMARK 3 S31: -0.0825 S32: 0.1293 S33: 0.0645 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. THE ADP-RIBSOYLLYSINE KETOAMINE AT RESIDUE B54 REMARK 3 REACHES INTO THE ACTIVE SITE OF THE CHAIN A SUBUNIT REMARK 4 REMARK 4 2WOD 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 DEPOSITION ID IS D_1290040048. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-SEP-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 : MAX II REMARK 200 BEAMLINE : I911-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43703 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 36.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.69000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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 (%): 61.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 81.86433 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 163.72867 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 163.72867 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 81.86433 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 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 -163.54 -117.82 REMARK 500 ARG A 94 70.99 49.91 REMARK 500 SER A 209 32.82 -144.77 REMARK 500 ALA A 291 -27.58 -39.64 REMARK 500 ARG B 43 11.63 -147.65 REMARK 500 THR B 59 -152.78 -128.08 REMARK 500 ARG B 94 75.97 53.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B2008 DISTANCE = 6.76 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 1'-DEOXY ADP-RIBOSYL (ZZC): C1' IS COVALENTLY LINKED TO THE REMARK 600 EPSILON-AMINO GROUP OF LYS54 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 ZZC A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZZC B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WOE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE D97N VARIANT OF DINITROGENASE REDUCTASE- REMARK 900 ACTIVATING GLYCOHYDROLASE (DRAG) FROM RHODOSPIRILLUM RUBRUM IN REMARK 900 COMPLEX WITH ADP-RIBOSE REMARK 900 RELATED ID: 2WOC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DINITROGENASE REDUCTASE-ACTIVATING REMARK 900 GLYCOHYDROLASE (DRAG) FROM RHODOSPIRILLUM RUBRUM DBREF 2WOD A -4 0 PDB 2WOD 2WOD -4 0 DBREF 2WOD A 1 294 UNP P14300 DRAG_RHORU 1 294 DBREF 2WOD B -4 0 PDB 2WOD 2WOD -4 0 DBREF 2WOD B 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 HET MN A 400 1 HET ZZC A 401 35 HET MN B 400 1 HET ZZC B 401 35 HET CL B 500 1 HET GOL B 600 6 HET GOL B 601 6 HETNAM MN MANGANESE (II) ION HETNAM ZZC [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY- HETNAM 2 ZZC OXOLAN-2-YL]METHYL [[(2R,3R)-2,3-DIHYDROXY-4-OXO- HETNAM 3 ZZC PENTOXY]-OXIDO-PHOSPHORYL] PHOSPHATE HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MN 2(MN 2+) FORMUL 4 ZZC 2(C15 H21 N5 O13 P2 2-) FORMUL 7 CL CL 1- FORMUL 8 GOL 2(C3 H8 O3) FORMUL 10 HOH *249(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 LINK NZ LYS B 54 C1'A ZZC A 401 1555 1555 1.47 CISPEP 1 GLU A 203 PRO A 204 0 -1.28 CISPEP 2 GLU B 203 PRO B 204 0 -4.41 SITE 1 AC1 6 ASP A 61 ASP A 243 THR A 246 ZZC A 401 SITE 2 AC1 6 HOH A2010 HOH A2034 SITE 1 AC2 27 ASP A 60 ASP A 97 GLY A 99 ASN A 100 SITE 2 AC2 27 THR A 101 CYS A 102 GLU A 121 GLY A 122 SITE 3 AC2 27 ALA A 124 GLY A 125 ASN A 126 GLY A 127 SITE 4 AC2 27 HIS A 158 ALA A 211 TYR A 212 ASP A 243 SITE 5 AC2 27 MN A 400 HOH A2034 HOH A2050 HOH A2099 SITE 6 AC2 27 HOH A2100 HOH A2101 HOH A2102 LYS B 54 SITE 7 AC2 27 ASP B 273 LYS B 275 HOH B2133 SITE 1 AC3 5 GLU B 28 ASP B 243 ASP B 245 THR B 246 SITE 2 AC3 5 ZZC B 401 SITE 1 AC4 18 ASP B 60 ASP B 97 GLY B 99 ASN B 100 SITE 2 AC4 18 THR B 101 CYS B 102 GLU B 121 GLY B 122 SITE 3 AC4 18 ALA B 124 GLY B 125 ASN B 126 GLY B 127 SITE 4 AC4 18 HIS B 158 TYR B 212 ASP B 243 THR B 246 SITE 5 AC4 18 MN B 400 HOH B2145 SITE 1 AC5 3 MET B 45 TRP B 268 GOL B 600 SITE 1 AC6 8 GLN A 37 GLN A 38 ARG B 43 LYS B 44 SITE 2 AC6 8 LYS B 231 GLY B 267 TRP B 268 CL B 500 SITE 1 AC7 6 HOH A2081 PRO B 55 LYS B 271 ASP B 273 SITE 2 AC7 6 HOH B2027 HOH B2127 CRYST1 77.306 77.306 245.593 90.00 90.00 120.00 P 31 2 1 12 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 0.012936 0.007468 0.000000 0.00000 SCALE2 0.000000 0.014937 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004072 0.00000 MTRIX1 1 -0.356000 -0.933000 -0.055000 60.48688 1 MTRIX2 1 0.918000 -0.360000 0.167000 -57.10409 1 MTRIX3 1 -0.176000 0.009000 0.984000 -3.98300 1