+Open data
-Basic information
Entry | Database: PDB / ID: 3ufh | ||||||
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Title | Crystal structure of UndA with Iron Citrate bound | ||||||
Components | UndA | ||||||
Keywords | TRANSPORT PROTEIN / C-type cytochrome / Electron transfer / c-type hemes / outermembrane | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shewanella sp. HRCR_06 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å | ||||||
Authors | Edwards, M.J. / Clarke, T.A. | ||||||
Citation | Journal: Structure / Year: 2012 Title: The Crystal Structure of the Extracellular 11-heme Cytochrome UndA Reveals a Conserved 10-heme Motif and Defined Binding Site for Soluble Iron Chelates. Authors: Edwards, M.J. / Hall, A. / Shi, L. / Fredrickson, J.K. / Zachara, J.M. / Butt, J.N. / Richardson, D.J. / Clarke, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ufh.cif.gz | 198.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ufh.ent.gz | 163.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ufh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ufh_validation.pdf.gz | 3.8 MB | Display | wwPDB validaton report |
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Full document | 3ufh_full_validation.pdf.gz | 3.8 MB | Display | |
Data in XML | 3ufh_validation.xml.gz | 42.2 KB | Display | |
Data in CIF | 3ufh_validation.cif.gz | 64.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/3ufh ftp://data.pdbj.org/pub/pdb/validation_reports/uf/3ufh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 92485.195 Da / Num. of mol.: 1 / Fragment: Soluble domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella sp. HRCR_06 (bacteria) / Gene: undA / Plasmid: pBAD / Production host: Shewanella oneidensis (bacteria) / Strain (production host): MR-1 / References: UniProt: F8UWD6 |
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-Non-polymers , 8 types, 850 molecules
#2: Chemical | ChemComp-HEC / #3: Chemical | #4: Chemical | ChemComp-CA / | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-O / | #8: Chemical | ChemComp-GOL / | #9: 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: 3.05 Å3/Da / Density % sol: 59.69 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M MES, 50 mM NaCl, 50 mM MgCl2, 15% PEG5000, 20% Glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.978 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2011 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→63.48 Å / Num. obs: 59175 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.5 / Redundancy: 3.4 % / Rsym value: 0.094 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.17→2.29 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.411 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→61.63 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.488 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.179 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.271 Å2
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Refinement step | Cycle: LAST / Resolution: 2.23→61.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.23→2.288 Å / Total num. of bins used: 20
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