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Yorodumi- PDB-4xkq: Crystal structure of NikA from Staphylococcus aureus in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xkq | ||||||
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Title | Crystal structure of NikA from Staphylococcus aureus in complex with Ni(L-His)2 (co-crystallization with Ni(II) and CD 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: 1.9 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 | 4xkq.cif.gz | 205.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xkq.ent.gz | 165.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xkq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/4xkq ftp://data.pdbj.org/pub/pdb/validation_reports/xk/4xkq | HTTPS FTP |
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-Related structure data
Related structure data | 4ofjSC 4xknC 4xkpC 4xkrC 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 19-461 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 , 5 types, 379 molecules
#2: Chemical | ChemComp-NI / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-EPE / | #6: 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: 2.28 Å3/Da / Density % sol: 45.96 % / 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 CD medium supernatant. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.00446 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00446 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45.77 Å / Num. obs: 39047 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rsym value: 0.11 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.14 / Rsym value: 0.799 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OFJ Resolution: 1.9→45.77 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.94 / 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: 24.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→45.77 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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