+Open data
-Basic information
Entry | Database: PDB / ID: 3mvx | ||||||
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Title | X-ray structure of the reduced NikA/1 hybrid, NikA/1-Red | ||||||
Components | Nickel-binding periplasmic protein | ||||||
Keywords | TRANSPORT PROTEIN / Protein-bound iron complex | ||||||
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: 1.7 Å | ||||||
Authors | Cavazza, C. / Bochot, C. / Rousselot-Pailley, P. / Carpentier, P. / Cherrier, M.V. / Martin, L. / Marchi-Delapierre, C. / Fontecilla-Camps, J.C. / Menage, S. | ||||||
Citation | Journal: NAT.CHEM. / Year: 2010 Title: Crystallographic snapshots of the reaction of aromatic C-H with O(2) catalysed by a protein-bound iron complex Authors: Cavazza, C. / Bochot, C. / Rousselot-Pailley, P. / Carpentier, P. / Cherrier, M.V. / Martin, L. / Marchi-Delapierre, C. / Fontecilla-Camps, J.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 | 3mvx.cif.gz | 226.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mvx.ent.gz | 180.2 KB | Display | PDB format |
PDBx/mmJSON format | 3mvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/3mvx ftp://data.pdbj.org/pub/pdb/validation_reports/mv/3mvx | HTTPS FTP |
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-Related structure data
Related structure data | 3mvwC 3mvyC 3mvzC 3mw0C 3mz9C 3mzbC 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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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) / Strain: K12 / Gene: nikA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33590, EC: 3.6.3.24 |
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-Non-polymers , 9 types, 755 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-SO4 / | #6: Chemical | ChemComp-GOL / #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-DTV / ( | #10: 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: 2.28 Å3/Da / Density % sol: 46.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 1.8M ammonium sulfate, 0.1M sodium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A |
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2008 / Details: Mirrors |
Radiation | Protocol: 0.9796 / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.7→47.3 Å / Num. obs: 110957 / % possible obs: 97 % / Redundancy: 7 % / Biso Wilson estimate: 25.6 Å2 / Rsym value: 0.056 / Net I/σ(I): 22.63 |
Reflection shell | Highest resolution: 1.7 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 5.9 / Num. unique all: 16443 / Rsym value: 0.315 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZLQ Resolution: 1.7→47.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.814 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R Free: 0.101 / 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 mean: 18.032 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→47.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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