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Yorodumi- PDB-5koh: Nitrogenase MoFeP from Gluconacetobacter diazotrophicus in dithio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5koh | ||||||||||||
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Title | Nitrogenase MoFeP from Gluconacetobacter diazotrophicus in dithionite reduced state | ||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / Nitrogenase / electron transfer / P-cluster | ||||||||||||
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 | Gluconacetobacter diazotrophicus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||||||||
Authors | Owens, C.P. / Tezcan, F.A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2016 Title: Tyrosine-Coordinated P-Cluster in G. diazotrophicus Nitrogenase: Evidence for the Importance of O-Based Ligands in Conformationally Gated Electron Transfer. Authors: Owens, C.P. / Katz, F.E. / Carter, C.H. / Oswald, V.F. / Tezcan, F.A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5koh.cif.gz | 450.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5koh.ent.gz | 359.5 KB | Display | PDB format |
PDBx/mmJSON format | 5koh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5koh_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5koh_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5koh_validation.xml.gz | 89.7 KB | Display | |
Data in CIF | 5koh_validation.cif.gz | 136.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/5koh ftp://data.pdbj.org/pub/pdb/validation_reports/ko/5koh | HTTPS FTP |
-Related structure data
Related structure data | 5kojC 1m1nS 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 56095.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Gluconacetobacter diazotrophicus (strain ATCC 49037 / DSM 5601 / PAl5) (bacteria) Strain: ATCC 49037 / DSM 5601 / PAl5 / References: UniProt: A9H5W5, nitrogenase #2: Protein | Mass: 57094.352 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Gluconacetobacter diazotrophicus (strain ATCC 49037 / DSM 5601 / PAl5) (bacteria) Strain: ATCC 49037 / DSM 5601 / PAl5 / References: UniProt: A9H5W8, nitrogenase |
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-Non-polymers , 7 types, 1990 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-MPD / ( | #9: 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 Å3/Da / Density % sol: 59.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 45% 2-methyl-2,4-pentadiol (MPD) , 300 mM NaCl, 100 mM Na Cacodylate, pH 6.5, 1 mM Spermine, 0.1% Zwittergent, and 5 mM Na2S2O4 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→143.26 Å / Num. obs: 240200 / % possible obs: 100 % / Redundancy: 27.2 % / Biso Wilson estimate: 14.27 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.4208 / Rsym value: 0.4288 / Net I/σ(I): 12.85 |
Reflection shell | Resolution: 1.83→1.895 Å / Redundancy: 27.8 % / Rmerge(I) obs: 1.434 / Mean I/σ(I) obs: 1.46 / CC1/2: 0.815 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1M1N Resolution: 1.83→143.26 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.676 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.078 / 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: 17.981 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→143.26 Å
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Refine LS restraints |
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