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Yorodumi- PDB-3qim: Histidine 416 of the periplamsic binding protein NikA is essentia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qim | ||||||
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Title | Histidine 416 of the periplamsic binding protein NikA is essential for nickel uptake in Escherichia coli | ||||||
Components | Nickel-binding periplasmic protein | ||||||
Keywords | TRANSPORT PROTEIN / METAL TRANSPORT | ||||||
Function / homology | Function and homology information nickel cation import across plasma membrane / metal cluster binding / peptide transport / peptide transmembrane transporter activity / negative chemotaxis / nickel cation binding / transition metal ion binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / periplasmic space ...nickel cation import across plasma membrane / metal cluster binding / peptide transport / peptide transmembrane transporter activity / negative chemotaxis / nickel cation binding / transition metal ion binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / periplasmic space / heme binding / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Cavazza, C. / Martin, L. / Laffly, E. / Lebrette, H. / Cherrier, M.V. / Zeppieri, L. / Richaud, P. / Carriere, M. / Fontecilla-Camps, J.C. | ||||||
Citation | Journal: Febs Lett. / Year: 2011 Title: Histidine 416 of the periplasmic binding protein NikA is essential for nickel uptake in Escherichia coli Authors: Cavazza, C. / Martin, L. / Laffly, E. / Lebrette, H. / Cherrier, M.V. / Zeppieri, L. / Richaud, P. / Carriere, M. / Fontecilla-Camps, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qim.cif.gz | 219.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qim.ent.gz | 176.2 KB | Display | PDB format |
PDBx/mmJSON format | 3qim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/3qim ftp://data.pdbj.org/pub/pdb/validation_reports/qi/3qim | HTTPS FTP |
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-Related structure data
Related structure data | 1zlqS 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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-Components
#1: Protein | Mass: 56335.746 Da / Num. of mol.: 2 / Mutation: H416I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b3476, JW3441, nikA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33590 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-SO4 / #5: 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: 2.25 Å3/Da / Density % sol: 45.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 1.6M Ammonium sulfate, 100 mM sodium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.984 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 23, 2010 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→24.84 Å / Num. obs: 56622 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 27.4 Å2 / Rsym value: 0.06 / Net I/σ(I): 12.93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZLQ Resolution: 2.1→24.84 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.966 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.411 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→24.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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