+Open data
-Basic information
Entry | Database: PDB / ID: 5vq3 | ||||||
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Title | Nitrogenase Cp1 at pH 6.5 | ||||||
Components | (Nitrogenase molybdenum-iron protein ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / Nitrogenase / Molybdenum-iron protein / MoFe protein / Cp1 | ||||||
Function / homology | Function and homology information molybdenum-iron nitrogenase complex / nitrogenase / : / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Clostridium pasteurianum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Morrison, C.N. / Spatzal, T. / Rees, D.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2017 Title: Reversible Protonated Resting State of the Nitrogenase Active Site. Authors: Morrison, C.N. / Spatzal, T. / Rees, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vq3.cif.gz | 402.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vq3.ent.gz | 324.6 KB | Display | PDB format |
PDBx/mmJSON format | 5vq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vq3_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5vq3_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5vq3_validation.xml.gz | 72.1 KB | Display | |
Data in CIF | 5vq3_validation.cif.gz | 102.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/5vq3 ftp://data.pdbj.org/pub/pdb/validation_reports/vq/5vq3 | HTTPS FTP |
-Related structure data
Related structure data | 5vpwC 5vq4C 4wesS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Nitrogenase molybdenum-iron protein ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 57870.910 Da / Num. of mol.: 2 / Fragment: UNP residues 1-520 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Gene: nifD / Production host: Escherichia coli (E. coli) / References: UniProt: P00467, nitrogenase #2: Protein | Mass: 50175.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Gene: nifK / Production host: Escherichia coli (E. coli) / References: UniProt: P11347, nitrogenase |
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-Non-polymers , 5 types, 679 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.66 Å3/Da / Density % sol: 53.73 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: PEG 3350, magnesium chloride, Tris/HCl, sodium dithionite |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→113.46 Å / Num. obs: 238230 / % possible obs: 98.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.72→1.75 Å / Redundancy: 7 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 11793 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WES Resolution: 1.72→40 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.073 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.257 Å2
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Refinement step | Cycle: 1 / Resolution: 1.72→40 Å
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Refine LS restraints |
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