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Yorodumi- PDB-4ofj: Crystal structure of NikA from Staphylococcus aureus in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ofj | ||||||
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Title | Crystal structure of NikA from Staphylococcus aureus in complex with Ni(L-His)2 | ||||||
Components | Extracytoplasmic Nickel-Binding Protein SaNikA | ||||||
Keywords | TRANSPORT PROTEIN / Extracytoplasmic / Nickel import / Metal transport / ABC-type importer / extracytoplasmic nickel-binding protein | ||||||
Function / homology | Function and homology information nickel cation transport / peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 | 4ofj.cif.gz | 212.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ofj.ent.gz | 169.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ofj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ofj_validation.pdf.gz | 460.5 KB | Display | wwPDB validaton report |
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Full document | 4ofj_full_validation.pdf.gz | 464.7 KB | Display | |
Data in XML | 4ofj_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 4ofj_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/4ofj ftp://data.pdbj.org/pub/pdb/validation_reports/of/4ofj | HTTPS FTP |
-Related structure data
Related structure data | 4xknC 4xkpC 4xkqC 4xkrC 3rqtS 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: subsp. aureus COL / Gene: SACOL0217 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HJE1, UniProt: Q2G2P5*PLUS |
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-Non-polymers , 5 types, 436 molecules
#2: Chemical | ChemComp-NI / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-EPE / | #5: Chemical | ChemComp-GOL / #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: 2.26 Å3/Da / Density % sol: 45.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 27 % PEG 3350, 0.1 M HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å |
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Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→45.69 Å / Num. all: 54220 / Num. obs: 53990 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rsym value: 0.079 / Net I/σ(I): 17.04 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 4.23 / Num. unique all: 8418 / Rsym value: 0.652 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RQT Resolution: 1.7→45.689 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 16.57 / 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: 1.7→45.689 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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