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Yorodumi- PDB-3e3k: Structural characterization of a putative endogenous metal chelat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e3k | ||||||
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Title | Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (butane-1,2,4-tricarboxylate without nickel form) | ||||||
Components | Nickel-binding periplasmic protein | ||||||
Keywords | METAL TRANSPORT / Nickel / nickellophore / butane-1 / 2 / 4-tricarboxylate / 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 / molecular replacement / Resolution: 2.8 Å | ||||||
Authors | Cherrier, M.V. / Cavazza, C. / Bochot, C. / Lemaire, D. / Fontecilla-Camps, J.C. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA Authors: Cherrier, M.V. / Cavazza, C. / Bochot, C. / Lemaire, D. / 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 | 3e3k.cif.gz | 279.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e3k.ent.gz | 229.9 KB | Display | PDB format |
PDBx/mmJSON format | 3e3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e3k_validation.pdf.gz | 513.5 KB | Display | wwPDB validaton report |
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Full document | 3e3k_full_validation.pdf.gz | 584.4 KB | Display | |
Data in XML | 3e3k_validation.xml.gz | 63.2 KB | Display | |
Data in CIF | 3e3k_validation.cif.gz | 84.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/3e3k ftp://data.pdbj.org/pub/pdb/validation_reports/e3/3e3k | HTTPS FTP |
-Related structure data
Related structure data | 3dp8C 1zlqS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 56360.734 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: nikA, b3476, JW3441 / Plasmid: pET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33590 |
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-Non-polymers , 6 types, 120 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-SO4 / | #5: Chemical | #6: Chemical | ChemComp-CL / #7: 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: 2.89 Å3/Da / Density % sol: 57.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 1.5M ammonium sulfate, 0.1M sodium acetate, pH4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 2007 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.8 Å / % possible obs: 93.6 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 64.602 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 5 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 5.3 / Num. measured obs: 45255 / Num. unique all: 4202 / Num. unique obs: 9081 / % possible all: 89.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZLQ Resolution: 2.8→48.45 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.85 / Occupancy min: 0 / SU B: 18.96 / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.36 / ESU R Free: 0.472 / 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 max: 86.29 Å2 / Biso mean: 61.426 Å2 / Biso min: 19.93 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→48.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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