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Yorodumi- PDB-7a0c: X-ray structure of NikA from Escherichia coli in complex with Fe-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a0c | ||||||
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Title | X-ray structure of NikA from Escherichia coli in complex with Fe-6-Me2-BPMCN | ||||||
Components | Nickel-binding periplasmic protein | ||||||
Keywords | METAL BINDING PROTEIN / Artificial metalloenzyme / cross-linked enzyme crystal / sulfoxidation | ||||||
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: Chemistry / Year: 2020 Title: A Selective Sulfide Oxidation Catalyzed by Heterogeneous Artificial Metalloenzymes Iron@NikA. Authors: Lopez, S. / Marchi-Delapierre, C. / 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 | 7a0c.cif.gz | 231.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a0c.ent.gz | 183.6 KB | Display | PDB format |
PDBx/mmJSON format | 7a0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a0c_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7a0c_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7a0c_validation.xml.gz | 45.7 KB | Display | |
Data in CIF | 7a0c_validation.cif.gz | 67.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/7a0c ftp://data.pdbj.org/pub/pdb/validation_reports/a0/7a0c | 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 (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 , 7 types, 823 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.24 Å3/Da / Density % sol: 45.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.7 M Ammonium sulfate, 100 mM sodium acetate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9799 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9799 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→43.875 Å / Num. obs: 80337 / % possible obs: 99.8 % / Redundancy: 5.3 % / CC1/2: 0.998 / Rsym value: 9.6 / Net I/σ(I): 13.06 |
Reflection shell | Resolution: 1.9→2 Å / Num. unique obs: 11314 / CC1/2: 0.655 / Rsym value: 1.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZLQ Resolution: 1.9→43.875 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.17 Å2 / Biso mean: 30.3509 Å2 / Biso min: 12.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→43.875 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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