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Yorodumi- PDB-1lyq: Crystal Structure of PcoC, a Methionine Rich Copper Resistance Pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lyq | ||||||
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Title | Crystal Structure of PcoC, a Methionine Rich Copper Resistance Protein from Escherichia coli | ||||||
Components | PcoC copper resistance protein | ||||||
Keywords | METAL BINDING PROTEIN / BETA BARREL / IG DOMAIN | ||||||
Function / homology | Function and homology information copper ion transport / response to copper ion / periplasmic space / copper ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Wernimont, A.K. / Huffman, D.L. / Finney, L.A. / Demeler, B. / O'Halloran, T.V. / Rosenzweig, A.C. | ||||||
Citation | Journal: J.BIOL.INORG.CHEM. / Year: 2003 Title: Crystal structure and dimerization equilibria of PcoC, a methionine-rich copper resistance protein from Escherichia coli Authors: Wernimont, A.K. / Huffman, D.L. / Finney, L.A. / Demeler, B. / O'Halloran, T.V. / Rosenzweig, A.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lyq.cif.gz | 61.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lyq.ent.gz | 45.4 KB | Display | PDB format |
PDBx/mmJSON format | 1lyq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lyq_validation.pdf.gz | 449 KB | Display | wwPDB validaton report |
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Full document | 1lyq_full_validation.pdf.gz | 462 KB | Display | |
Data in XML | 1lyq_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 1lyq_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/1lyq ftp://data.pdbj.org/pub/pdb/validation_reports/ly/1lyq | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11063.694 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: plasmid pRJ1004 / Plasmid: pDLHII265 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q47454 #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.28 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 81 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 31, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→35 Å / Num. all: 30640 / Num. obs: 29303 / % possible obs: 95.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.075 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.45→1.49 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2399 / Rsym value: 0.278 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb from MAD solution Resolution: 1.5→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 18.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.57 Å / Rfactor Rfree error: 0.013
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