+Open data
-Basic information
Entry | Database: PDB / ID: 5abr | ||||||
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Title | Structure of FeSI protein from Azotobacter vinelandii | ||||||
Components | FERREDOXIN, 2FE-2S | ||||||
Keywords | ELECTRON TRANSPORT / FERREDOXIN | ||||||
Function / homology | Function and homology information : / nitrogen fixation / 2 iron, 2 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | AZOTOBACTER VINELANDII (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.11 Å | ||||||
Authors | Kabasakal, B. / Murray, J.W. | ||||||
Citation | Journal: To be Published Title: Structure of Fesi Protein from Azotobacter Vinelandii Authors: Kabasakal, B. / Cotton, C.A.R. / Murray, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5abr.cif.gz | 96.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5abr.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 5abr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/5abr ftp://data.pdbj.org/pub/pdb/validation_reports/ab/5abr | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 13438.304 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AZOTOBACTER VINELANDII (bacteria) / Strain: DSM-2289 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Plasmid: PRSETA / Production host: ESCHERICHIA COLI KRX (bacteria) / References: UniProt: P82802 #2: Chemical | #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: 2.09 Å3/Da / Density % sol: 41.24 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 100 MM HEPES PH 7.5, 77% V/V MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.73404 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Feb 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.73404 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→42.93 Å / Num. obs: 11386 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.11→2.16 Å / Redundancy: 3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.4 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.11→42.934 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / SU B: 12.183 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.11→42.934 Å
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Refine LS restraints |
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