+Open data
-Basic information
Entry | Database: PDB / ID: 2nip | ||||||
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Title | NITROGENASE IRON PROTEIN FROM AZOTOBACTER VINELANDII | ||||||
Components | NITROGENASE IRON PROTEIN | ||||||
Keywords | IRON PROTEIN / OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information nitrogenase / carbonyl sulfide nitrogenase activity / nitrogenase activity / nitrogen fixation / 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 | Komiya, H. / Georgiadis, M.M. / Chakrabarti, P. / Woo, D. / Kornuc, J.J. / Rees, D.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Conformational variability in structures of the nitrogenase iron proteins from Azotobacter vinelandii and Clostridium pasteurianum. Authors: Schlessman, J.L. / Woo, D. / Joshua-Tor, 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 | 2nip.cif.gz | 124 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nip.ent.gz | 99.1 KB | Display | PDB format |
PDBx/mmJSON format | 2nip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/2nip ftp://data.pdbj.org/pub/pdb/validation_reports/ni/2nip | HTTPS FTP |
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-Related structure data
Related structure data | 1cp2C 1nipS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 31417.045 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: OP / References: UniProt: P00459, nitrogenase #2: Chemical | ChemComp-SF4 / | #3: 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: 2.4 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: liquid-liquid diffusion / pH: 8 Details: PROTEIN WAS CRYSTALLIZED BY LIQUID-LIQUID DIFFUSION METHOD, USING 25-30% PEG 4000, 140-200 MM NA2MOO4, 100 MM TRIS-CL, PH 8.0; PROTEIN WAS HELD IN A BUFFER OF 20% GLYCEROL, 50 MM TRIS-CL, PH ...Details: PROTEIN WAS CRYSTALLIZED BY LIQUID-LIQUID DIFFUSION METHOD, USING 25-30% PEG 4000, 140-200 MM NA2MOO4, 100 MM TRIS-CL, PH 8.0; PROTEIN WAS HELD IN A BUFFER OF 20% GLYCEROL, 50 MM TRIS-CL, PH 8.0, 450 MM NACL, AND 2 MM NA2S2O4 PRIOR TO CRYSTALLIZATION., liquid-liquid diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1995 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→50 Å / Num. obs: 29060 / % possible obs: 92.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.309 / % possible all: 94.9 |
Reflection | *PLUS Num. measured all: 260578 |
Reflection shell | *PLUS % possible obs: 94.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NIP Resolution: 2.2→50 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 31.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.29 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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