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Yorodumi- PDB-3dp8: Structural characterization of a putative endogenous metal chelat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dp8 | ||||||
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Title | Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (nickel butane-1,2,4-tricarboxylate 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 transmembrane transporter activity / peptide transport / 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 transmembrane transporter activity / peptide transport / 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: 2.5 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 | 3dp8.cif.gz | 312.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dp8.ent.gz | 256.5 KB | Display | PDB format |
PDBx/mmJSON format | 3dp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dp8_validation.pdf.gz | 519 KB | Display | wwPDB validaton report |
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Full document | 3dp8_full_validation.pdf.gz | 577.4 KB | Display | |
Data in XML | 3dp8_validation.xml.gz | 64.5 KB | Display | |
Data in CIF | 3dp8_validation.cif.gz | 86.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/3dp8 ftp://data.pdbj.org/pub/pdb/validation_reports/dp/3dp8 | HTTPS FTP |
-Related structure data
Related structure data | 3e3kC 1zlqS 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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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: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33590 |
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-Non-polymers , 7 types, 298 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-CL / #6: Chemical | #7: Chemical | ChemComp-GOL / #8: 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: 2.9 Å3/Da / Density % sol: 57.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 1.5M ammonium sulfate, 100mM 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: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2005 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 64541 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rsym value: 0.046 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 5.4 / Num. measured obs: 20248 / Num. unique all: 13530 / Num. unique obs: 6977 / Rsym value: 0.326 |
-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: 2.5→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 0 / SU B: 10.21 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.466 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 100.84 Å2 / Biso mean: 51.118 Å2 / Biso min: 17.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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