+Open data
-Basic information
Entry | Database: PDB / ID: 8k7n | ||||||
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Title | Structure of ferric-binding protein KfuA | ||||||
Components | Ferric iron ABC transporter, iron-binding protein | ||||||
Keywords | METAL BINDING PROTEIN / Iron binding protein / ABC transporter | ||||||
Function / homology | Function and homology information transmembrane transport / outer membrane-bounded periplasmic space / iron ion transport / metal ion binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Zhao, Q. / Bartlam, M. | ||||||
Funding support | China, 1items
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Citation | Journal: To be published Title: Structure of Klebsiella pneumoniae ferric-binding protein KfuA Authors: Zhao, Q. / Bartlam, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k7n.cif.gz | 80.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k7n.ent.gz | 56.8 KB | Display | PDB format |
PDBx/mmJSON format | 8k7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/8k7n ftp://data.pdbj.org/pub/pdb/validation_reports/k7/8k7n | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36585.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Sequence reference for Klebsiella pneumoniae is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A288TNX3. Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: fbpA, CWN47_21360, IAP99_17305, NCTC9178_03966 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A288TNX3 |
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#2: Chemical | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.23 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Sodium chloride, 25% w/v Polyethylene glycol 3,350 and 0.1 M Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→38.29 Å / Num. obs: 18079 / % possible obs: 96.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 22.78 Å2 / Rpim(I) all: 0.031 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2→2.03 Å / Num. unique obs: 882 / Rpim(I) all: 0.073 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.58 Å / SU ML: 0.1684 / Cross valid method: FREE R-VALUE / σ(F): 0.41 / Phase error: 19.3347 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→37.58 Å
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Refine LS restraints |
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LS refinement shell |
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