+Open data
-Basic information
Entry | Database: PDB / ID: 2afi | ||||||
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Title | Crystal Structure of MgADP bound Av2-Av1 Complex | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Nitrogen fixation / Iron-sulfur / Metal-binding / Molybdenum | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Tezcan, F.A. / Kaiser, J.T. / Mustafi, D. / Walton, M.Y. / Howard, J.B. / Rees, D.C. | ||||||
Citation | Journal: Science / Year: 2005 Title: Nitrogenase Complexes: Multiple Docking Sites for a Nucleotide Switch Protein Authors: Tezcan, F.A. / Kaiser, J.T. / Mustafi, D. / Walton, M.Y. / Howard, J.B. / Rees, D.C. | ||||||
History |
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Remark 600 | HETEROGEN The Ca atom 2492 is associated with water molecules 9000, 9001, the Ca atom 4492 is ...HETEROGEN The Ca atom 2492 is associated with water molecules 9000, 9001, the Ca atom 4492 is associated with water molecules 9002, 9003, the Ca atom 6492 is associated with water molecules 9004, 9005 and the Ca atom 8492 is associated with water molecules 9006, 9007. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2afi.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2afi.ent.gz | 975.4 KB | Display | PDB format |
PDBx/mmJSON format | 2afi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2afi_validation.pdf.gz | 4.3 MB | Display | wwPDB validaton report |
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Full document | 2afi_full_validation.pdf.gz | 4.5 MB | Display | |
Data in XML | 2afi_validation.xml.gz | 214.3 KB | Display | |
Data in CIF | 2afi_validation.cif.gz | 286.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/2afi ftp://data.pdbj.org/pub/pdb/validation_reports/af/2afi | HTTPS FTP |
-Related structure data
Related structure data | 2afhC 4wzbC 1m1nS 2nipS 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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2 |
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Unit cell |
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-Components
-Nitrogenase molybdenum-iron ... , 2 types, 8 molecules ACIKBDJL
#1: Protein | Mass: 55231.848 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: alpha chain / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07328, nitrogenase #2: Protein | Mass: 59404.684 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: beta chain / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase |
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-Protein , 1 types, 8 molecules EFGHMNOP
#3: Protein | Mass: 31417.045 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P00459, nitrogenase |
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-Non-polymers , 8 types, 44 molecules
#4: Chemical | ChemComp-HCA / #5: Chemical | ChemComp-CFN / #6: Chemical | ChemComp-CA / #7: Chemical | ChemComp-CLF / #8: Chemical | ChemComp-MG / #9: Chemical | ChemComp-ADP / #10: Chemical | ChemComp-SF4 / #11: 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: 2.25 Å3/Da / Density % sol: 44.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG8000, Sodium Chloride, Magnesium Chloride, ADP, Dithionite, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. all: 97281 / Num. obs: 97281 / % possible obs: 88.2 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 1.7 % / Rsym value: 0.075 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 3.1→3.2 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.242 / % possible all: 72 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M1N, 2NIP Resolution: 3.1→49.43 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2770509.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The residues in the coordinates with 0 occupancy were not located in the experiments
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.5046 Å2 / ksol: 0.27916 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→49.43 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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