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Yorodumi- PDB-2bdq: Crystal Structure of the Putative Copper Homeostasis Protein CutC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bdq | ||||||
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Title | Crystal Structure of the Putative Copper Homeostasis Protein CutC from Streptococcus agalactiae, Northeast Strucural Genomics Target SaR15. | ||||||
Components | copper homeostasis protein CutC | ||||||
Keywords | METAL TRANSPORT / alpha beta protein / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus agalactiae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Forouhar, F. / Abashidze, M. / Jayaraman, S. / Ho, C.K. / Cooper, B. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Putative Copper Homeostasis Protein CutC from Streptococcus agalactiae, Northeast Strucural Genomics Target SaR15. Authors: Forouhar, F. / Abashidze, M. / Jayaraman, S. / Ho, C.K. / Cooper, B. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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Remark 999 | SEQUENCE Residue 212 is a modified residue and a cloning artifact. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bdq.cif.gz | 92.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bdq.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 2bdq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/2bdq ftp://data.pdbj.org/pub/pdb/validation_reports/bd/2bdq | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25220.861 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: 2603V-R / Gene: SAG1569 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8DYB9 #2: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 44.14 % Description: The reflections reported in data collection include friedel pairs |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10 mM Tris, 18% PEG3350, 200 mM NaSCN, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2005 / Details: mirrors. |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 38496 / Num. obs: 36017 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.109 / Net I/σ(I): 19.71 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 9.61 / Num. unique all: 2013 / Rsym value: 0.329 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→29.25 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 395954.69 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Friedel pairs have been used in refinement
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.4141 Å2 / ksol: 0.332444 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 23 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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