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Yorodumi- PDB-1n2c: NITROGENASE COMPLEX FROM AZOTOBACTER VINELANDII STABILIZED BY ADP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n2c | ||||||
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Title | NITROGENASE COMPLEX FROM AZOTOBACTER VINELANDII STABILIZED BY ADP-TETRAFLUOROALUMINATE | ||||||
Components |
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Keywords | COMPLEX OF NITROGENASE PROTEINS / NITROGENASE / NITROGEN FIXATION / SIGNAL TRANSDUCTION / ELECTRON TRANSFER / ATP HYDROLYSIS | ||||||
Function / homology | Function and homology information molybdenum-iron nitrogenase complex / nitrogenase / : / 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 / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Schindelin, H. / Kisker, C. / Rees, D.C. | ||||||
Citation | Journal: Nature / Year: 1997 Title: Structure of ADP x AIF4(-)-stabilized nitrogenase complex and its implications for signal transduction. Authors: Schindelin, H. / Kisker, C. / Schlessman, J.L. / 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 | 1n2c.cif.gz | 544.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n2c.ent.gz | 444.1 KB | Display | PDB format |
PDBx/mmJSON format | 1n2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n2c_validation.pdf.gz | 731.3 KB | Display | wwPDB validaton report |
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Full document | 1n2c_full_validation.pdf.gz | 795.4 KB | Display | |
Data in XML | 1n2c_validation.xml.gz | 66.2 KB | Display | |
Data in CIF | 1n2c_validation.cif.gz | 96.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/1n2c ftp://data.pdbj.org/pub/pdb/validation_reports/n2/1n2c | HTTPS FTP |
-Related structure data
Related structure data | 1min 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 oper:
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-Components
-NITROGENASE MOLYBDENUM-IRON ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 55231.848 Da / Num. of mol.: 2 Fragment: CHAINS A AND C ARE THE ALPHA CHAINS, CHAINS B AND D ARE THE BETA CHAINS Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07328, nitrogenase #2: Protein | Mass: 59404.684 Da / Num. of mol.: 2 Fragment: CHAINS A AND C ARE THE ALPHA CHAINS, CHAINS B AND D ARE THE BETA CHAINS 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: 31417.045 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: 2\:1 COMPLEX OF HOMODIMERIC FE-PROTEIN AND HETEROTETRAMERIC MOFE-PROTEIN Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P00459, nitrogenase |
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-Non-polymers , 8 types, 22 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-MG / #9: Chemical | ChemComp-ALF / #10: Chemical | ChemComp-ADP / #11: Chemical | |
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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: 2.8 Å3/Da / Density % sol: 55.5 % | ||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 16-20% PEG 8000, 0.1 M CACODYLATE PH 6.5 AND 20-50 MM MGCL2 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 57735 / % possible obs: 73.8 % / Redundancy: 1.8 % / Rsym value: 0.098 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 3→3.11 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.245 / % possible all: 28.8 |
Reflection | *PLUS Num. measured all: 104037 / Rmerge(I) obs: 0.098 |
Reflection shell | *PLUS % possible obs: 28.8 % / Rmerge(I) obs: 0.245 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MIN 1min Resolution: 3→50 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Isotropic thermal model: ONE B-FACTOR PER RESIDUE / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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