[English] 日本語
Yorodumi- PDB-4oes: Crystal structure of NikA from Brucella suis in complex with Fe(I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oes | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of NikA from Brucella suis in complex with Fe(III)-EDTA | ||||||
Components | NikA protein | ||||||
Keywords | TRANSPORT PROTEIN / Extracytoplasmic / Nickel import / Metal transport / ABC-type importer / extracytoplasmic nickel-binding protein | ||||||
Function / homology | Function and homology information nickel cation transport / nickel cation binding / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space / heme binding Similarity search - Function | ||||||
Biological species | Brucella suis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 Å | ||||||
Authors | Lebrette, H. / Cavazza, C. | ||||||
Citation | Journal: Structure / Year: 2014 Title: Promiscuous nickel import in human pathogens: structure, thermodynamics, and evolution of extracytoplasmic nickel-binding proteins. Authors: Lebrette, H. / Brochier-Armanet, C. / Zambelli, B. / de Reuse, H. / Borezee-Durant, E. / Ciurli, S. / Cavazza, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4oes.cif.gz | 218.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4oes.ent.gz | 173.1 KB | Display | PDB format |
PDBx/mmJSON format | 4oes.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oes_validation.pdf.gz | 853.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4oes_full_validation.pdf.gz | 856.1 KB | Display | |
Data in XML | 4oes_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 4oes_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/4oes ftp://data.pdbj.org/pub/pdb/validation_reports/oe/4oes | HTTPS FTP |
-Related structure data
Related structure data | 4oerSC 4oetC 4oeuC 4oevC 4oflC 4ofoC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55540.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella suis (bacteria) / Gene: nikA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AL82 |
---|
-Non-polymers , 5 types, 399 molecules
#2: Chemical | ChemComp-EDT / {[-( | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-FE / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.31 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2.0 M ammonium sulfate, 0.1 M Tris pH 8.5, 25 mM MgSO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97973 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2011 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97973 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→46.85 Å / Num. all: 44102 / Num. obs: 43076 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.077 / Net I/σ(I): 10.96 |
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.45 / Num. unique all: 6132 / Rsym value: 0.356 / % possible all: 93.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4OER Resolution: 1.951→46.845 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 26.55 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.951→46.845 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|