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Yorodumi- PDB-4xkr: Crystal structure of NikA from Staphylococcus aureus in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xkr | ||||||
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Title | Crystal structure of NikA from Staphylococcus aureus in complex with Ni-(L-His)(2-methyl-thiazolidine dicarboxylate) (co-crystallization with Ni(II) and CDdeltaHis medium supernatant) | ||||||
Components | Nickel ABC transporter substrate-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / Extracytoplasmic Nickel-Binding Protein / Nickel import / ABC-type importer | ||||||
Function / homology | Function and homology information nickel cation transport / peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Staphylococcus aureus USA300-ISMMS1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Lebrette, H. / Cavazza, C. | ||||||
Citation | Journal: Metallomics / Year: 2015 Title: Novel insights into nickel import in Staphylococcus aureus: the positive role of free histidine and structural characterization of a new thiazolidine-type nickel chelator. Authors: Lebrette, H. / Borezee-Durant, E. / Martin, L. / Richaud, P. / Boeri Erba, E. / Cavazza, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xkr.cif.gz | 213.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xkr.ent.gz | 170.4 KB | Display | PDB format |
PDBx/mmJSON format | 4xkr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xkr_validation.pdf.gz | 475.9 KB | Display | wwPDB validaton report |
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Full document | 4xkr_full_validation.pdf.gz | 480.1 KB | Display | |
Data in XML | 4xkr_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 4xkr_validation.cif.gz | 38.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/4xkr ftp://data.pdbj.org/pub/pdb/validation_reports/xk/4xkr | HTTPS FTP |
-Related structure data
Related structure data | 4ofjSC 4xknC 4xkpC 4xkqC S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 53545.285 Da / Num. of mol.: 1 / Fragment: UNP residues 19-491 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus USA300-ISMMS1 (bacteria) Gene: AZ30_01190 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W6DY02, UniProt: Q2G2P5*PLUS |
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-Non-polymers , 7 types, 546 molecules
#2: Chemical | ChemComp-NI / | ||||
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#3: Chemical | ChemComp-HIS / | ||||
#4: Chemical | ChemComp-41K / ( | ||||
#5: Chemical | ChemComp-EPE / | ||||
#6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.25 % / Description: plate |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 27% PEG 3350, 0.1 M HEPES pH 7.0 - protein pre-incubated with NiCl2 and CDdeltaHis medium supernatant. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→45.54 Å / Num. obs: 47766 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rsym value: 0.078 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.36 / Rsym value: 0.616 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OFJ Resolution: 1.75→45.543 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.33 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→45.543 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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