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Yorodumi- PDB-5ovo: Structure of DraG-GlnZ-delta42-54 complex from Azospirillum brasilense -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ovo | ||||||
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Title | Structure of DraG-GlnZ-delta42-54 complex from Azospirillum brasilense | ||||||
Components |
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Keywords | METAL BINDING PROTEIN / Glycohydrolase | ||||||
Function / homology | Function and homology information ADP-ribosyl-[dinitrogen reductase] hydrolase / ADP-ribosyl-[dinitrogen reductase] hydrolase activity / regulation of nitrogen utilization / metabolic process / enzyme regulator activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Azospirillum brasilense (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å | ||||||
Authors | Berthold, C.L. / Hogbom, M. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: To Be Published Title: Structure of DraG-GlnZ-delta42-54 complex from Azospirillum brasilense Authors: Berthold, C.L. / Hogbom, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ovo.cif.gz | 102.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ovo.ent.gz | 80 KB | Display | PDB format |
PDBx/mmJSON format | 5ovo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/5ovo ftp://data.pdbj.org/pub/pdb/validation_reports/ov/5ovo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32442.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azospirillum brasilense (bacteria) / Gene: draG, AMK58_04675 / Production host: Escherichia coli (E. coli) / References: UniProt: A7XNI2 |
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#2: Protein | Mass: 10801.536 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azospirillum brasilense (bacteria) / Gene: glnZ, ABAZ39_13575, AMK58_13670 / Production host: Escherichia coli (E. coli) / References: UniProt: P70731 |
-Non-polymers , 4 types, 512 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MN / | #6: Water | ChemComp-HOH / | |
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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: 61.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion Details: 35 % (v/v) glycerol ethoxylate, 0.2 M lithium citrate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 7, 2014 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.55→46.8 Å / Num. obs: 77898 / % possible obs: 99.8 % / Redundancy: 5.2 % / Rpim(I) all: 0.05 / Net I/σ(I): 10.9 |
-Processing
Software |
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Refinement | Resolution: 1.55→45.6 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.703 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.012 / ESU R Free: 0.012 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.895 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→45.6 Å
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Refine LS restraints |
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