+Open data
-Basic information
Entry | Database: PDB / ID: 1cp2 | ||||||
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Title | NITROGENASE IRON PROTEIN FROM CLOSTRIDIUM PASTEURIANUM | ||||||
Components | NITROGENASE IRON PROTEIN | ||||||
Keywords | OXIDOREDUCTASE / NITROGENASE IRON PROTEIN | ||||||
Function / homology | Function and homology information nitrogenase / : / nitrogenase activity / nitrogen fixation / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Clostridium pasteurianum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Schlessman, J.L. / Woo, D. / Joshua-Tor, L. / Howard, J.B. / 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 | 1cp2.cif.gz | 114.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cp2.ent.gz | 88.7 KB | Display | PDB format |
PDBx/mmJSON format | 1cp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cp2_validation.pdf.gz | 394.6 KB | Display | wwPDB validaton report |
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Full document | 1cp2_full_validation.pdf.gz | 409.8 KB | Display | |
Data in XML | 1cp2_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 1cp2_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/1cp2 ftp://data.pdbj.org/pub/pdb/validation_reports/cp/1cp2 | HTTPS FTP |
-Related structure data
Related structure data | 2nipC 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: 29219.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: COVALENT BRIDGE BETWEEN CYS 94 AND CYS 129 GAMMA SULFURS AND THE FE'S OF 4FE4S CLUSTER Source: (natural) Clostridium pasteurianum (bacteria) / Cell line: W5 / References: UniProt: P00456, 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: 2.18 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: liquid - liquid diffusion / pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED BY LIQUID-LIQUID DIFFUSION METHOD. PRECIPITANT CONTAINED 5-15% GLYCEROL, 18.75-22.5% PEG 4000, 230-270 MM CACL2, AND 50 MM HEPES PH 7.5. PROTEIN WAS STORED BEFORE ...Details: PROTEIN WAS CRYSTALLIZED BY LIQUID-LIQUID DIFFUSION METHOD. PRECIPITANT CONTAINED 5-15% GLYCEROL, 18.75-22.5% PEG 4000, 230-270 MM CACL2, AND 50 MM HEPES PH 7.5. PROTEIN WAS STORED BEFORE CRYSTALLIZATION IN 20% GLYCEROL, 50 MM HEPES, PH 7.5, AND 2 MM NA2S2O4., 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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 1, 1993 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→15.63 Å / Num. obs: 36808 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.0725 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.93→2 Å / % possible all: 91 |
Reflection | *PLUS Num. measured all: 250737 |
Reflection shell | *PLUS % possible obs: 91 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NIP Resolution: 1.93→5 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 36.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→2 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
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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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