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- PDB-3mvz: X-ray structure of the (hydro)peroxo intermediate NikA/1-Int", af... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mvz | ||||||
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Title | X-ray structure of the (hydro)peroxo intermediate NikA/1-Int", after monohydroxylation of the iron complex | ||||||
![]() | Nickel-binding periplasmic protein | ||||||
![]() | TRANSPORT PROTEIN / Protein-bound iron complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cavazza, C. / Bochot, C. / Rousselot-Pailley, P. / Carpentier, P. / Cherrier, M.V. / Martin, L. / Marchi-Delapierre, C. / Fontecilla-Camps, J.C. / Menage, S. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 239.5 KB | Display | ![]() |
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PDB format | ![]() | 189.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 50.7 KB | Display | |
Data in CIF | ![]() | 76.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mvwC ![]() 3mvxC ![]() 3mvyC ![]() 3mw0C ![]() 3mz9C ![]() 3mzbC ![]() 1zlqS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 1120 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/BHN.gif)
![](data/chem/img/PER.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/BHN.gif)
![](data/chem/img/PER.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 1.8M ammonium acetate, 0.1M sodium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 26, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→47.2 Å / Num. obs: 105943 / % possible obs: 93 % / Redundancy: 2.7 % / Biso Wilson estimate: 24.6 Å2 / Rsym value: 0.063 / Net I/σ(I): 11.2 |
Reflection shell | Highest resolution: 1.7 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 29711 / Rsym value: 0.293 / % possible all: 93 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ZLQ Resolution: 1.7→47.15 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.856 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R Free: 0.103 / 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: 17.236 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→47.15 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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