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Yorodumi- PDB-3cp0: Crystal structure of the soluble domain of membrane protein impli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cp0 | ||||||
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Title | Crystal structure of the soluble domain of membrane protein implicated in regulation of membrane protease activity from Corynebacterium glutamicum | ||||||
Components | Membrane protein implicated in regulation of membrane protease activityBiological membrane | ||||||
Keywords | MEMBRANE PROTEIN / beta barrel / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Protease | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Corynebacterium glutamicum ATCC 13032 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å | ||||||
Authors | Kim, Y. / Tesar, C. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of the soluble domain of membrane protein implicated in regulation of membrane protease activity from Corynebacterium glutamicum. Authors: Kim, Y. / Tesar, C. / Abdullah, J. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cp0.cif.gz | 24.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cp0.ent.gz | 18.5 KB | Display | PDB format |
PDBx/mmJSON format | 3cp0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/3cp0 ftp://data.pdbj.org/pub/pdb/validation_reports/cp/3cp0 | 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 8923.986 Da / Num. of mol.: 1 / Fragment: CG1731 domain: Residues 64-142 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria) Species: Corynebacterium glutamicum / Strain: DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025 / Gene: cg1731 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6M555, UniProt: Q8NQA4*PLUS | ||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #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: 2.04 Å3/Da / Density % sol: 39.59 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.05 M Zinc acetate dihydrate, 20% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2008 / Details: Mirrors |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→40 Å / Num. all: 9137 / Num. obs: 9137 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 20.43 Å2 / Rsym value: 0.113 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.22 / % possible all: 86.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.65→33.2 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.126 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.097 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.127 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→33.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 19.7791 Å / Origin y: 3.1642 Å / Origin z: 25.9387 Å
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