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Yorodumi- PDB-1zlq: Crystallographic and spectroscopic evidence for high affinity bin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zlq | ||||||
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Title | Crystallographic and spectroscopic evidence for high affinity binding of Fe EDTA (H2O)- to the periplasmic nickel transporter NikA | ||||||
Components | Nickel-binding periplasmic protein | ||||||
Keywords | HYDROLASE / Nickel / EDTA / Transport / bacteria | ||||||
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: 1.8 Å | ||||||
Authors | Cherrier, M.V. / Martin, L. / Cavazza, C. / Jacquamet, L. / Lemaire, D. / Gaillard, J. / Fontecilla Camps, J.C. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2005 Title: Crystallographic and Spectroscopic Evidence for High Affinity Binding of FeEDTA(H(2)O)(-) to the Periplasmic Nickel Transporter NikA Authors: Cherrier, M.V. / Martin, L. / Cavazza, C. / Jacquamet, L. / Lemaire, D. / Gaillard, J. / 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 | 1zlq.cif.gz | 439.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zlq.ent.gz | 358.2 KB | Display | PDB format |
PDBx/mmJSON format | 1zlq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/1zlq ftp://data.pdbj.org/pub/pdb/validation_reports/zl/1zlq | HTTPS FTP |
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-Related structure data
Related structure data | 1uivS 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 56360.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nikA / Plasmid: pet22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P33590, EC: 3.6.3.24 |
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-Non-polymers , 8 types, 884 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-CL / #6: Chemical | #7: Chemical | ChemComp-DTT / | #8: Chemical | ChemComp-GOL / #9: 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: 2.5 Å3/Da / Density % sol: 50.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: Ammonium Sulfate/Sodium acetate, pH 4.7, temperature 293K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 6, 2005 |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9756 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→39.2 Å / Num. all: 94047 / Num. obs: 92472 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 17.96 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.304 / Num. unique all: 43603 / Rsym value: 0.304 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UIV Resolution: 1.8→39.2 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 20.566 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→39.2 Å
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Refine LS restraints |
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