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Yorodumi- PDB-4oxr: Structure of Staphylococcus pseudintermedius metal-binding protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oxr | ||||||
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Title | Structure of Staphylococcus pseudintermedius metal-binding protein SitA in complex with Manganese | ||||||
Components | Manganese ABC transporter, periplasmic-binding protein SitA | ||||||
Keywords | METAL BINDING PROTEIN / Manganese binding protein / SBP / ABC transporter | ||||||
Function / homology | Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : / : Function and homology information | ||||||
Biological species | Staphylococcus pseudintermedius (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Abate, F. / Malito, E. / Bottomley, M. | ||||||
Citation | Journal: Biosci.Rep. / Year: 2014 Title: Apo, Zn2+-bound and Mn2+-bound structures reveal ligand-binding properties of SitA from the pathogen Staphylococcus pseudintermedius. Authors: Abate, F. / Malito, E. / Cozzi, R. / Lo Surdo, P. / Maione, D. / Bottomley, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oxr.cif.gz | 126.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oxr.ent.gz | 96.6 KB | Display | PDB format |
PDBx/mmJSON format | 4oxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oxr_validation.pdf.gz | 427.5 KB | Display | wwPDB validaton report |
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Full document | 4oxr_full_validation.pdf.gz | 431.1 KB | Display | |
Data in XML | 4oxr_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 4oxr_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/4oxr ftp://data.pdbj.org/pub/pdb/validation_reports/ox/4oxr | HTTPS FTP |
-Related structure data
Related structure data | 4oxqC 1pszS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 29 - 306 / Label seq-ID: 8 - 285
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-Components
#1: Protein | Mass: 32187.090 Da / Num. of mol.: 2 / Fragment: ectodomain (UNP residues 23-306) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus pseudintermedius (bacteria) Strain: IV369-1041 / Gene: SPSE_2131 / Plasmid: pET-15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F0P9H5 #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 Å3/Da / Density % sol: 39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1,1,1,3,3,3-hexafluoro-2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.45 Å / Num. obs: 33582 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 16.69 Å2 / Rsym value: 0.116 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 4.7 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PSZ Resolution: 2→39.417 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→39.417 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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