+Open data
-Basic information
Entry | Database: PDB / ID: 6z8q | ||||||
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Title | Copper transporter OprC | ||||||
Components | Putative copper transport outer membrane porin OprC | ||||||
Keywords | MEMBRANE PROTEIN / copper transporter / TBDT / Pseudomonas aeruginosa / OprC | ||||||
Function / homology | Function and homology information siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / cell outer membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Bhamidimarri, S.P. / van den Berg, B. | ||||||
Citation | Journal: Plos Biol. / Year: 2021 Title: Acquisition of ionic copper by the bacterial outer membrane protein OprC through a novel binding site. Authors: Bhamidimarri, S.P. / Young, T.R. / Shanmugam, M. / Soderholm, S. / Basle, A. / Bumann, D. / van den Berg, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z8q.cif.gz | 319.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z8q.ent.gz | 207.1 KB | Display | PDB format |
PDBx/mmJSON format | 6z8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z8q_validation.pdf.gz | 415.8 KB | Display | wwPDB validaton report |
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Full document | 6z8q_full_validation.pdf.gz | 430 KB | Display | |
Data in XML | 6z8q_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 6z8q_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/6z8q ftp://data.pdbj.org/pub/pdb/validation_reports/z8/6z8q | HTTPS FTP |
-Related structure data
Related structure data | 6fokSC 6fomC 6z8rC 6z8sC 6z8tC 6z8uC 6z8yC 6z8zC 6z91C 6z99C 6z9nC 6z9yC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 79395.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: oprC, PA3790 / Production host: Escherichia coli (E. coli) / References: UniProt: G3XD89 #2: Chemical | ChemComp-AG / #3: Water | ChemComp-HOH / | 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: 4.02 Å3/Da / Density % sol: 69.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M NaCl 0.15 M NH4SO4 0.1 M MES 18-22% PEG1000 2 mM AgNO3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.54977 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54977 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→121.98 Å / Num. obs: 69478 / % possible obs: 99.99 % / Redundancy: 35.5 % / Biso Wilson estimate: 75.71 Å2 / Rpim(I) all: 0.028 / Net I/σ(I): 20.12 |
Reflection shell | Resolution: 2.71→2.76 Å / Num. unique obs: 6843 / CC1/2: 0.653 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FOK Resolution: 2.71→97.65 Å / SU ML: 0.3698 / Cross valid method: FREE R-VALUE / σ(F): 0.34 / Phase error: 27.1843 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 79.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.71→97.65 Å
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Refine LS restraints |
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LS refinement shell |
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