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Yorodumi- PDB-3w5j: Crystal structure of GDP-bound NfeoB from Gallionella capsiferrif... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w5j | ||||||
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Title | Crystal structure of GDP-bound NfeoB from Gallionella capsiferriformans | ||||||
Components | Ferrous iron transport protein B | ||||||
Keywords | METAL TRANSPORT / G PROTEIN / IRON TRANSPORT / GTPASE / TRANSMEMBRANE / GDP | ||||||
Function / homology | Function and homology information ferrous iron transmembrane transporter activity / GTP binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Gallionella capsiferriformans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.932 Å | ||||||
Authors | Deshpande, C.N. / McGrath, A.P. / Jormakka, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Structure of an atypical FeoB G-domain reveals a putative domain-swapped dimer. Authors: Deshpande, C.N. / McGrath, A.P. / Font, J. / Guilfoyle, A.P. / Maher, M.J. / Jormakka, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w5j.cif.gz | 93.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w5j.ent.gz | 68.9 KB | Display | PDB format |
PDBx/mmJSON format | 3w5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/3w5j ftp://data.pdbj.org/pub/pdb/validation_reports/w5/3w5j | HTTPS FTP |
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-Related structure data
Related structure data | 3w5iC 3ibyS 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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Unit cell |
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-Components
#1: Protein | Mass: 22732.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallionella capsiferriformans (bacteria) Strain: ES-2 / Gene: Galf_2203 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D9SIP4 #2: Chemical | ChemComp-GDP / | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-SO4 / | #5: 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: 2.02 Å3/Da / Density % sol: 39.06 % / Mosaicity: 0.67 ° |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2M Ammonium sulphate, 0.1M Bis-Tris pH 5.5, 25 % (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 24, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.93→63.08 Å / Num. all: 28390 / Num. obs: 28390 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 18.2 Å2 / Rsym value: 0.151 / Net I/σ(I): 9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3IBY Resolution: 1.932→47.72 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2235 / WRfactor Rwork: 0.1858 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8692 / SU B: 3.711 / SU ML: 0.108 / SU R Cruickshank DPI: 0.1798 / SU Rfree: 0.1574 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 53.06 Å2 / Biso mean: 23.4563 Å2 / Biso min: 7.19 Å2
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Refinement step | Cycle: LAST / Resolution: 1.932→47.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.932→1.982 Å / Total num. of bins used: 20
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