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Yorodumi- PDB-7jj9: Crystal structure of Zn(II)-bound AdcA from Streptococcus pneumoniae -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jj9 | |||||||||||||||
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Title | Crystal structure of Zn(II)-bound AdcA from Streptococcus pneumoniae | |||||||||||||||
Components | Zinc-binding lipoprotein AdcA | |||||||||||||||
Keywords | METAL BINDING PROTEIN / AdcA / SBP / ATP-binding cassette transporter / Zn acquisition | |||||||||||||||
Function / homology | Function and homology information zinc ion transport / establishment of competence for transformation / cell adhesion / zinc ion binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Streptococcus pneumoniae (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | |||||||||||||||
Authors | Luo, Z. / More, J.R. / Kobe, B. / McDevitt, C.A. | |||||||||||||||
Funding support | Australia, 4items
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Citation | Journal: Mbio / Year: 2021 Title: A Trap-Door Mechanism for Zinc Acquisition by Streptococcus pneumoniae AdcA. Authors: Luo, Z. / Morey, J.R. / Deplazes, E. / Motygullina, A. / Tan, A. / Ganio, K. / Neville, S.L. / Eleftheriadis, N. / Isselstein, M. / Pederick, V.G. / Paton, J.C. / Cordes, T. / Harmer, J.R. / ...Authors: Luo, Z. / Morey, J.R. / Deplazes, E. / Motygullina, A. / Tan, A. / Ganio, K. / Neville, S.L. / Eleftheriadis, N. / Isselstein, M. / Pederick, V.G. / Paton, J.C. / Cordes, T. / Harmer, J.R. / Kobe, B. / McDevitt, C.A. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jj9.cif.gz | 199.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jj9.ent.gz | 156.1 KB | Display | PDB format |
PDBx/mmJSON format | 7jj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/7jj9 ftp://data.pdbj.org/pub/pdb/validation_reports/jj/7jj9 | HTTPS FTP |
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-Related structure data
Related structure data | 7jj8C 7jjaC 7jjbC 2osvS 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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Unit cell |
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-Components
#1: Protein | Mass: 53545.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria) Strain: ATCC BAA-255 / R6 / Gene: adcA, spr1975 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CWN2 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: 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: 2.21 Å3/Da / Density % sol: 44.29 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% w/v polyethylene glycol 20000, 18% v/v PEG monomethyl ether 550, 0.03 M CaCl2, 0.03 M MgCl2, 0.1 M MES/imidazole pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→19.84 Å / Num. obs: 64356 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 13.8320172758 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.096 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.58→1.61 Å / Rmerge(I) obs: 0.843 / Num. unique obs: 275 / CC1/2: 0.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OSV Resolution: 1.58→19.83 Å / SU ML: 0.15851032789 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.4721589407 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: 21.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→19.83 Å
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Refine LS restraints |
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LS refinement shell |
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