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Yorodumi- PDB-5mwu: Crystal structure of the periplasmic nickel-binding protein NikA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mwu | ||||||
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Title | Crystal structure of the periplasmic nickel-binding protein NikA from Escherichia coli in complex with Ru(bpza)(CO)2Cl | ||||||
Components | Nickel-binding periplasmic protein | ||||||
Keywords | METAL BINDING PROTEIN / Artificial metalloenzymes / chlorine insertion / chlorhydrins / bio-inspired chemistry | ||||||
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 K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Cavazza, C. / Lopez, S. / Rondot, L. / Iannello, M. / Boeri-Erba, E. / Burzlaff, N. / Strinitz, F. / Jorge-Robin, A. / Marchi-Delapierre, C. / Menage, S. | ||||||
Funding support | France, 1items
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Citation | Journal: To Be Published Title: Efficient conversion of alkenes to chlorohydrins by a Ru-based artificial enzyme Authors: Lopez, S. / Rondot, L. / Cavazza, C. / Iannello, M. / Boeri-Erba, E. / Burzlaff, N. / Strinitz, N. / Jorge-Robin, A. / Marchi-Delapierre, 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 | 5mwu.cif.gz | 230.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mwu.ent.gz | 182.1 KB | Display | PDB format |
PDBx/mmJSON format | 5mwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mwu_validation.pdf.gz | 888.9 KB | Display | wwPDB validaton report |
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Full document | 5mwu_full_validation.pdf.gz | 903.4 KB | Display | |
Data in XML | 5mwu_validation.xml.gz | 45.7 KB | Display | |
Data in CIF | 5mwu_validation.cif.gz | 67.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mw/5mwu ftp://data.pdbj.org/pub/pdb/validation_reports/mw/5mwu | HTTPS FTP |
-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 K12 (bacteria) / Gene: nikA, b3476, JW3441 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33590 |
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-Non-polymers , 10 types, 697 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-FE / | #6: Chemical | ChemComp-EDT / {[-( | #7: Chemical | ChemComp-RU / | #8: Chemical | #9: Chemical | ChemComp-6RP / | #10: Chemical | #11: 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: 2.23 Å3/Da / Density % sol: 44.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 15 mg/ml protei solution mixed with 1.8 M ammonium sulfate, 100 mM sodium acetate pH 4.7 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979769 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979769 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→46.8 Å / Num. obs: 92563 / % possible obs: 98.8 % / Redundancy: 4.98 % / Biso Wilson estimate: 27.6 Å2 / Rsym value: 0.057 / Net I/σ(I): 21.24 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZLQ Resolution: 1.8→46.8 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.145 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.121 / 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: 27.073 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→46.8 Å
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Refine LS restraints |
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