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- PDB-3c8i: Crystal structure of a putative membrane protein from Corynebacte... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3c8i | ||||||
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Title | Crystal structure of a putative membrane protein from Corynebacterium diphtheriae | ||||||
![]() | Putative membrane protein | ||||||
![]() | MEMBRANE PROTEIN / putative membrane protein / Corynebacterium diphtheriae / Structural genomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | putative membrane protein from Corynebacterium diphtheriae fold / putative membrane protein from Corynebacterium diphtheriae superfamily / Protein of unknown function DUF3239 / DUF3239 domain superfamily / Protein of unknown function (DUF3239) / membrane => GO:0016020 / Beta Barrel / Mainly Beta / Putative membrane protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, R. / Hatzos, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: The crystal structure of a putative membrane protein from Corynebacterium diphtheriae. Authors: Zhang, R. / Hatzos, C. / Clancy, S. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.8 KB | Display | ![]() |
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PDB format | ![]() | 47.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.3 KB | Display | ![]() |
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Full document | ![]() | 435.3 KB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15545.565 Da / Num. of mol.: 2 / Fragment: Residues 75-215 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Corynebacterium diphtheriae / Strain: NCTC 13129 / Biotype gravis / Gene: GI:38199630, DIP0771 / Plasmid: pDM68 / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.19 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.05M Calcium chloride dihydrate, 0.1M Bis-Tris, 30% v/v PEG MME 550, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2007 / Details: Mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→62.26 Å / Num. all: 22137 / Num. obs: 22035 / % possible obs: 99.54 % / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Biso Wilson estimate: 28.01 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 40.13 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 2.31 / Num. unique all: 1702 / % possible all: 99.94 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 27.602 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→62.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -1.318 Å / Origin y: 18.336 Å / Origin z: 16.523 Å
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Refinement TLS group |
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