+Open data
-Basic information
Entry | Database: PDB / ID: 8k8l | ||||||
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Title | Structure of Klebsiella pneumonia ModA with molybdate | ||||||
Components | Molybdate transporter periplasmic protein | ||||||
Keywords | METAL BINDING PROTEIN / Molybdate binding protein | ||||||
Function / homology | Molybdate ABC transporter, substrate-binding protein / molybdate ion transport / Bacterial extracellular solute-binding protein / metal ion binding / MOLYBDATE ION / Molybdate transporter periplasmic protein Function and homology information | ||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Zhao, Q. / Bartlam, M. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2023 Title: Structural analysis of molybdate binding protein ModA from Klebsiella pneumoniae. Authors: Zhao, Q. / Su, X. / Wang, Y. / Liu, R. / Bartlam, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k8l.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k8l.ent.gz | 44.8 KB | Display | PDB format |
PDBx/mmJSON format | 8k8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k8l_validation.pdf.gz | 768 KB | Display | wwPDB validaton report |
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Full document | 8k8l_full_validation.pdf.gz | 769.8 KB | Display | |
Data in XML | 8k8l_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 8k8l_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/8k8l ftp://data.pdbj.org/pub/pdb/validation_reports/k8/8k8l | HTTPS FTP |
-Related structure data
Related structure data | 8k8kC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27008.760 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (strain HS11286) (bacteria) Gene: KPHS_16010 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3GU89 |
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#2: Chemical | ChemComp-MOO / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.12 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 3 Details: 0.1 M Citric acid, 25% w/v Polyethylene glycol 3,350, molybdate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→50 Å / Num. obs: 20631 / % possible obs: 98.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 18.64 Å2 / Rpim(I) all: 0.036 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.77→1.83 Å / Num. unique obs: 2045 / Rpim(I) all: 0.149 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→28.76 Å / SU ML: 0.1844 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 19.7607 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→28.76 Å
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Refine LS restraints |
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LS refinement shell |
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