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Yorodumi- PDB-8au6: Structure of Corynebacterium glutamicum Cg1604, a cell division r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8au6 | ||||||
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Title | Structure of Corynebacterium glutamicum Cg1604, a cell division regulator | ||||||
Components | Regulatory protein Cg1604 | ||||||
Keywords | CELL CYCLE / bacterial cell division / peptidoglycan hydrolysis / regulatory protein | ||||||
Function / homology | Copper transporter MctB / Copper transport outer membrane protein, MctB / copper ion homeostasis / membrane / Copper transporter Function and homology information | ||||||
Biological species | Corynebacterium glutamicum ATCC 13032 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Gaday, Q. / Wehenkel, A.M. / Alzari, P.M. | ||||||
Funding support | France, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: FtsEX-independent control of RipA-mediated cell separation in Corynebacteriales. Authors: Gaday, Q. / Megrian, D. / Carloni, G. / Martinez, M. / Sokolova, B. / Ben Assaya, M. / Legrand, P. / Brule, S. / Haouz, A. / Wehenkel, A.M. / Alzari, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8au6.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8au6.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 8au6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8au6_validation.pdf.gz | 420.1 KB | Display | wwPDB validaton report |
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Full document | 8au6_full_validation.pdf.gz | 420.2 KB | Display | |
Data in XML | 8au6_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 8au6_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/8au6 ftp://data.pdbj.org/pub/pdb/validation_reports/au/8au6 | HTTPS FTP |
-Related structure data
Related structure data | 8aucC 8audC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 32802.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria) Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025 Gene: Cgl1416 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NQL8 |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.06 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 30 % (w/v) PEG 4K, 0.2 M MgCl2, 0.1 M TRIS pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979261 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979261 Å / Relative weight: 1 |
Reflection | Resolution: 2→44.1 Å / Num. obs: 17209 / % possible obs: 99.7 % / Redundancy: 14.6 % / CC1/2: 0.999 / Rpim(I) all: 0.035 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 11.5 % / Num. unique obs: 1207 / CC1/2: 0.551 / Rpim(I) all: 0.642 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→44.04 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.52 Å2 / Biso mean: 48.0537 Å2 / Biso min: 29.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→44.04 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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