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Yorodumi- PDB-4m1p: Crystal structure of the copper-sensing repressor CsoR with Cu(I)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m1p | ||||||
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Title | Crystal structure of the copper-sensing repressor CsoR with Cu(I) from Geobacillus thermodenitrificans NG80-2 | ||||||
Components | Copper-sensitive operon repressor (CsoR) | ||||||
Keywords | TRANSCRIPTION REPRESSOR / Cu(I)-sensing transcriptional repressor / Cu(I) binding | ||||||
Function / homology | Function and homology information regulation of DNA-templated transcription / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Geobacillus thermodenitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.564 Å | ||||||
Authors | Chang, F. / Dann III, C.E. / Giedroc, D.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Cu(I)-mediated allosteric switching in a copper-sensing operon repressor (CsoR). Authors: Chang, F.M. / Coyne, H.J. / Cubillas, C. / Vinuesa, P. / Fang, X. / Ma, Z. / Ma, D. / Helmann, J.D. / Garcia-de los Santos, A. / Wang, Y.X. / Dann, C.E. / Giedroc, D.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m1p.cif.gz | 52.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m1p.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 4m1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m1p_validation.pdf.gz | 415.6 KB | Display | wwPDB validaton report |
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Full document | 4m1p_full_validation.pdf.gz | 415.6 KB | Display | |
Data in XML | 4m1p_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 4m1p_validation.cif.gz | 6.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/4m1p ftp://data.pdbj.org/pub/pdb/validation_reports/m1/4m1p | HTTPS FTP |
-Related structure data
Related structure data | 4adzS S: Starting model for refinement |
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Similar 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: 11946.913 Da / Num. of mol.: 1 / Mutation: T2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria) Strain: NG80-2 / Gene: GTNG_1533 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21(DE3) / References: UniProt: A4INJ9 | ||
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#2: Chemical | ChemComp-CU1 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.87 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.8M sodium formate, 0.1M HEPES, 0.1M betaine hydrochloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: May 9, 2013 / Details: Sagitally focused mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→50 Å / Num. all: 4463 / Num. obs: 4463 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 30.91 |
Reflection shell | Resolution: 2.57→2.61 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.94 / Num. unique all: 4463 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4ADZ Resolution: 2.564→46.375 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.564→46.375 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -28.579 Å / Origin y: 45.5563 Å / Origin z: 70.6202 Å
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Refinement TLS group | Selection details: all |