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Yorodumi- PDB-2wod: Crystal Structure of the dinitrogenase reductase-activating glyco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wod | ||||||
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Title | Crystal Structure of the dinitrogenase reductase-activating glycohydrolase (DRAG) from Rhodospirillum rubrum in complex with ADP- ribsoyllysine | ||||||
Components | ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE | ||||||
Keywords | HYDROLASE / NITROGEN FIXATION / DIMANGANESE-DEPENDENT / ADP-RIBOSYLGLYCOHYDROLASE / MONO-ADP-RIBOSYLHYDROLASE | ||||||
Function / homology | Function and homology information ADP-ribosyl-[dinitrogen reductase] hydrolase / ADP-ribosyl-[dinitrogen reductase] hydrolase activity / protein de-ADP-ribosylation / nitrogen fixation / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | RHODOSPIRILLUM RUBRUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Berthold, C.L. / Wang, H. / Nordlund, S. / Hogbom, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Mechanism of Adp-Ribosylation Removal Revealed by the Structure and Ligand Complexes of the Dimanganese Mono-Adp-Ribosylhydrolase Drag. Authors: Berthold, C.L. / Wang, H. / Nordlund, S. / Hogbom, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wod.cif.gz | 122.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wod.ent.gz | 100.2 KB | Display | PDB format |
PDBx/mmJSON format | 2wod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/2wod ftp://data.pdbj.org/pub/pdb/validation_reports/wo/2wod | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.356, -0.933, -0.055), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 32244.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: LYS B54 IS MONO-ADP-RIBOSYLATED / Source: (gene. exp.) RHODOSPIRILLUM RUBRUM (bacteria) / Strain: S1 / Plasmid: PGEX-6P-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) STAR References: UniProt: P14300, ADP-ribosyl-[dinitrogen reductase] hydrolase |
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-Non-polymers , 5 types, 256 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | 1'-DEOXY ADP-RIBOSYL (ZZC): C1' IS COVALENTLY |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.99 |
Detector | Date: Sep 11, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→36.86 Å / Num. obs: 43703 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.1 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→34.92 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 13.081 / SU ML: 0.169 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ADP-RIBSOYLLYSINE KETOAMINE AT RESIDUE B54 REACHES INTO THE ACTIVE SITE OF THE CHAIN A SUBUNIT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.532 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→34.92 Å
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Refine LS restraints |
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