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Yorodumi- PDB-7li0: Crystal structure of apo Moraxella catarrhalis ferric binding pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7li0 | ||||||
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Title | Crystal structure of apo Moraxella catarrhalis ferric binding protein A in an open conformation | ||||||
Components | Fe(3+) ABC transporter substrate-binding protein | ||||||
Keywords | METAL TRANSPORT / ferric binding protein A / FbpA | ||||||
Function / homology | Ferric binding protein / metal ion binding / CITRIC ACID / CARBONATE ION / DI(HYDROXYETHYL)ETHER / Fe(3+) ABC transporter substrate-binding protein Function and homology information | ||||||
Biological species | Moraxella catarrhalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Chan, C. / Ng, D. / Fraser, M.E. / Schryvers, A.B. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Biometals / Year: 2022 Title: Structural and functional insights into iron acquisition from lactoferrin and transferrin in Gram-negative bacterial pathogens. Authors: Chan, C. / Ng, D. / Fraser, M.E. / Schryvers, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7li0.cif.gz | 262.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7li0.ent.gz | 206.7 KB | Display | PDB format |
PDBx/mmJSON format | 7li0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7li0_validation.pdf.gz | 490.6 KB | Display | wwPDB validaton report |
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Full document | 7li0_full_validation.pdf.gz | 496 KB | Display | |
Data in XML | 7li0_validation.xml.gz | 50.8 KB | Display | |
Data in CIF | 7li0_validation.cif.gz | 72.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/7li0 ftp://data.pdbj.org/pub/pdb/validation_reports/li/7li0 | HTTPS FTP |
-Related structure data
Related structure data | 7li1C 6g7nS 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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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 34304.738 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moraxella catarrhalis (bacteria) / Gene: fbpA / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: A0A1E9VR34 |
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-Non-polymers , 6 types, 734 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-CIT / | #7: 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: 2.17 Å3/Da / Density % sol: 43.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M ammonium citrate tribasic pH 6.5, 30% v/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92009 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92009 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→51.61 Å / Num. obs: 96783 / % possible obs: 96.8 % / Redundancy: 1.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.058 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 1.84→1.87 Å / Rmerge(I) obs: 0.416 / Num. unique obs: 4682 / CC1/2: 0.795 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6G7N Resolution: 1.85→51.61 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 34.67 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→51.61 Å
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Refine LS restraints |
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