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Yorodumi- PDB-1x7i: Crystal structure of the native copper homeostasis protein (cutCm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x7i | ||||||
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Title | Crystal structure of the native copper homeostasis protein (cutCm) with calcium binding from Shigella flexneri 2a str. 301 | ||||||
Components | Copper homeostasis protein cutC | ||||||
Keywords | METAL BINDING PROTEIN / cutC family / Tim-like protein / Copper homeostasis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shigella flexneri 2a str. 301 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Zhu, D.Y. / Zhu, Y.Q. / Huang, R.H. / Xiang, Y. / Wang, D.C. | ||||||
Citation | Journal: Proteins / Year: 2004 Title: Crystal structure of the copper homeostasis protein (CutCm) from Shigella flexneri at 1.7 A resolution: The first structure of a new sequence family of TIM barrels Authors: Zhu, D.Y. / Zhu, Y.Q. / Huang, R.H. / Xiang, Y. / Yang, N. / Lu, H.X. / Li, G.P. / Jin, Q. / Wang, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x7i.cif.gz | 109.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x7i.ent.gz | 88.1 KB | Display | PDB format |
PDBx/mmJSON format | 1x7i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x7i_validation.pdf.gz | 439.6 KB | Display | wwPDB validaton report |
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Full document | 1x7i_full_validation.pdf.gz | 449.8 KB | Display | |
Data in XML | 1x7i_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 1x7i_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/1x7i ftp://data.pdbj.org/pub/pdb/validation_reports/x7/1x7i | HTTPS FTP |
-Related 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: 27863.936 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri 2a str. 301 (bacteria) Species: Shigella flexneri / Strain: 301 / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P67825 #2: Chemical | ChemComp-CA / | #3: 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: 2.19 Å3/Da / Density % sol: 43.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% PEG8000, 0.1M Sodium Cacodylate ph 6.0, 0.15M Calcium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97938, 0.97850, 0.97000, 0.9780 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2004 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→45.83 Å / Num. all: 52869 / Num. obs: 52833 / % possible obs: 1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 8.2 | |||||||||||||||
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 4.4 / Num. unique all: 7152 / Rsym value: 0.159 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→45.83 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2636661.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.1566 Å2 / ksol: 0.328693 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→45.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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