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Yorodumi- PDB-1g20: MGATP-BOUND AND NUCLEOTIDE-FREE STRUCTURES OF A NITROGENASE PROTE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g20 | ||||||
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Title | MGATP-BOUND AND NUCLEOTIDE-FREE STRUCTURES OF A NITROGENASE PROTEIN COMPLEX BETWEEN LEU127DEL-FE PROTEIN AND THE MOFE PROTEIN | ||||||
Components |
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Keywords | OXIDOREDUCTASE / nitrogen-fixation / Fe protein / MoFe protein / P-cluster and FeMo cofactor | ||||||
Function / homology | Function and homology information molybdenum-iron nitrogenase complex / nitrogenase / carbonyl sulfide nitrogenase activity / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Azotobacter vinelandii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Chiu, H.-J. / Peters, J.W. / Lanzilotta, W.N. / Ryle, M.J. / Seefeldt, L.C. / Howard, J.B. / Rees, D.C. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: MgATP-Bound and nucleotide-free structures of a nitrogenase protein complex between the Leu 127 Delta-Fe-protein and the MoFe-protein. Authors: Chiu, H. / Peters, J.W. / Lanzilotta, W.N. / Ryle, M.J. / Seefeldt, L.C. / Howard, J.B. / 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 | 1g20.cif.gz | 615.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g20.ent.gz | 499.3 KB | Display | PDB format |
PDBx/mmJSON format | 1g20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/1g20 ftp://data.pdbj.org/pub/pdb/validation_reports/g2/1g20 | HTTPS FTP |
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-Related structure data
Related structure data | 1g21C 2minS 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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Details | The biological assembly is a dimer, and each subunit contains one MoeFe protein and two Fe protein monomers |
-Components
-NITROGENASE MOLYBDENUM-IRON PROTEIN ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 55363.043 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07328, nitrogenase #2: Protein | Mass: 59535.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase |
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-Protein , 1 types, 4 molecules EFGH
#3: Protein | Mass: 31435.084 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P00459, nitrogenase |
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-Non-polymers , 6 types, 1076 molecules
#4: Chemical | #5: Chemical | #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: 2.5 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: microcapillary batch diffusion / pH: 8.5 Details: PEG 4000, sodium acetate, Tris-HCl. Ph 8.8, pH 8.5, microcapillary batch diffusion, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 20, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 167675 / Num. obs: 157699 / % possible obs: 89.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0.5 / Redundancy: 6.5 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.296 / % possible all: 83.2 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 94.7 % / Num. measured all: 1092580 |
Reflection shell | *PLUS % possible obs: 83.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2MIN Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 0.5 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.219 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |