[English] 日本語
Yorodumi- PDB-3k1a: Insights into substrate binding at FeMo-cofactor in nitrogenase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k1a | ||||||
---|---|---|---|---|---|---|---|
Title | Insights into substrate binding at FeMo-cofactor in nitrogenase from the structure of an alpha-70Ile MoFe protein variant | ||||||
Components | (Nitrogenase molybdenum-iron protein ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / NITROGEN FIXATION / MoFe protein / nitrogenase / isoleucine / 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 / carbonyl sulfide nitrogenase activity / 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: 2.23 Å | ||||||
Authors | Peters, J.W. / Sarma, R. / Barney, B.M. / Keable, S. / Seefeldt, L.C. / Dean, D.R. | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2010 Title: Insights into substrate binding at FeMo-cofactor in nitrogenase from the structure of an alpha-70(Ile) MoFe protein variant Authors: Sarma, R. / Barney, B.M. / Keable, S. / Dean, D.R. / Seefeldt, L.C. / Peters, J.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3k1a.cif.gz | 417.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3k1a.ent.gz | 335.2 KB | Display | PDB format |
PDBx/mmJSON format | 3k1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/3k1a ftp://data.pdbj.org/pub/pdb/validation_reports/k1/3k1a | HTTPS FTP |
---|
-Related structure data
Related structure data | 2minS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Nitrogenase molybdenum-iron protein ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 55245.875 Da / Num. of mol.: 2 / Mutation: V70I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: nifDK, nifK / Production host: Escherichia coli (E. coli) / References: UniProt: P07328, nitrogenase #2: Protein | Mass: 59404.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: nifD / Production host: Escherichia coli (E. coli) / References: UniProt: P07329, nitrogenase |
---|
-Non-polymers , 5 types, 838 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.12 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.89 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 21, 2008 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→50 Å / Num. obs: 187881 / % possible obs: 99.9 % / Observed criterion σ(I): 2.3 / Redundancy: 3.8 % / Rsym value: 0.115 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.23→2.33 Å / Redundancy: 3.5 % / Num. unique all: 18797 / Rsym value: 0.233 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2MIN Resolution: 2.23→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.233 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The Friedel pairs were used in phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 31.399 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.23→50 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.23→2.29 Å / Total num. of bins used: 20
|