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Yorodumi- PDB-6r4q: Crystal structure of the periplasmic nickel-binding protein NikA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r4q | ||||||
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Title | Crystal structure of the periplasmic nickel-binding protein NikA from Escherichia coli in complex with Ru(bpza)CO H2O Cl | ||||||
Components | Nickel-binding periplasmic protein | ||||||
Keywords | METAL BINDING PROTEIN / Artificial metalloenzyme / Ru-based oxidase / styrene oxidation | ||||||
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: 1.9 Å | ||||||
Authors | Cavazza, C. / Menage, S. | ||||||
Funding support | France, 1items
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Citation | Journal: To Be Published Title: Crystal structure of the periplasmic nickel-binding protein NikA from Escherichia coli in complex with Ru(bpza)CO H2O Cl Authors: Cavazza, C. / Menage, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r4q.cif.gz | 231.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r4q.ent.gz | 182 KB | Display | PDB format |
PDBx/mmJSON format | 6r4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/6r4q ftp://data.pdbj.org/pub/pdb/validation_reports/r4/6r4q | 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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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 (strain K12) (bacteria) Strain: K12 / Gene: nikA, b3476, JW3441 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33590 |
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-Non-polymers , 9 types, 772 molecules
#2: Chemical | ChemComp-FE / | ||||||||||||
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#3: Chemical | ChemComp-EDT / {[-( | ||||||||||||
#4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-ACT / #7: Chemical | ChemComp-RU / | #8: Chemical | ChemComp-6RP / | #9: Chemical | ChemComp-CMO / | #10: Water | ChemComp-HOH / | |
-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: 45.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1M Na acetate pH 4.6 1.8 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979758 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979758 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.52 Å / Num. obs: 564360 / % possible obs: 99.9 % / Redundancy: 7 % / Net I/σ(I): 16.06 |
Reflection shell | Resolution: 1.9→2 Å / Num. unique obs: 11369 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZLQ Resolution: 1.9→44.52 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.208 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.152 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.17 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→44.52 Å
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