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Yorodumi- PDB-4xpi: Fe protein independent substrate reduction by nitrogenase variant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xpi | ||||||
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Title | Fe protein independent substrate reduction by nitrogenase variants altered in intramolecular electron transfer | ||||||
Components | (Nitrogenase molybdenum-iron protein ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / NITROGEN FIXATION / MoFe protein / nitrogenase / proton reduction / nitrogen / acetylene / hydride reduction / ATP-binding / Iron / Iron-sulfur / Metal-binding / Nucleotide-binding / Molybdenum | ||||||
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 | Azotobacter vinelandii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Danyal, K. / Rasmusen, A.J. / Keable, S.M. / Shaw, S. / Zadvornyy, O. / Duval, S. / Dean, D.R. / Raugei, S. / Peters, J.W. / Seefeldt, L.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2015 Title: Fe protein-independent substrate reduction by nitrogenase MoFe protein variants. Authors: Danyal, K. / Rasmussen, A.J. / Keable, S.M. / Inglet, B.S. / Shaw, S. / Zadvornyy, O.A. / Duval, S. / Dean, D.R. / Raugei, S. / Peters, J.W. / Seefeldt, L.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xpi.cif.gz | 820.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xpi.ent.gz | 674.5 KB | Display | PDB format |
PDBx/mmJSON format | 4xpi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xpi_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 4xpi_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 4xpi_validation.xml.gz | 87.2 KB | Display | |
Data in CIF | 4xpi_validation.cif.gz | 120.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/4xpi ftp://data.pdbj.org/pub/pdb/validation_reports/xp/4xpi | HTTPS FTP |
-Related structure data
Related structure data | 3u7qS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Nitrogenase molybdenum-iron protein ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 55130.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: nifD / Production host: Azotobacter vinelandii (bacteria) / Strain (production host): DJ939 / References: UniProt: P07328, nitrogenase #2: Protein | Mass: 59379.652 Da / Num. of mol.: 2 / Mutation: Y98H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: nifK / Production host: Azotobacter vinelandii (bacteria) / Strain (production host): DJ939 / References: UniProt: P07329, nitrogenase |
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-Non-polymers , 7 types, 946 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Chemical | #8: Chemical | #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: 2.29 Å3/Da / Density % sol: 46.4 % |
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Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 8 Details: 30% PEG 4000, 100mM Tris-HCl pH 8.0, 170-190mM Sodium molybdate and 1mM Dithionite, LIQUID DIFFUSION, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 4, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→35.8 Å / Num. obs: 141514 / % possible obs: 96.39 % / Redundancy: 3.5 % / Net I/σ(I): 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3U7Q Resolution: 1.97→35 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.25 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.191 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.796 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→35 Å
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Refine LS restraints |
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