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- PDB-3cxj: Crystal structure of an uncharacterized protein from Methanotherm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3cxj | ||||||
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Title | Crystal structure of an uncharacterized protein from Methanothermobacter thermautotrophicus | ||||||
![]() | Uncharacterized protein | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / 10518a / PSI-II / Uncharacterized protein / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Protein of unknown function DUF2299 / Uncharacterized conserved protein (DUF2299) / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sugadev, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: Crystal structure of an uncharacterized protein from Methanothermobacter thermautotrophicus. Authors: Sugadev, R. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.4 KB | Display | ![]() |
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PDB format | ![]() | 106.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.4 KB | Display | ![]() |
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Full document | ![]() | 480.2 KB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 35.5 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19914.359 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: Delta H / Gene: MTH1410 / Plasmid: pSGX3(BC) / 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: 2.63 Å3/Da / Density % sol: 53.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 1.5 M Lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2008 / Details: Mirrors |
Radiation | Monochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 24954 / Num. obs: 24954 / % possible obs: 80.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 50.1 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 1 / Num. unique all: 867 / % possible all: 28.9 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled ...Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines. The R free is slightly high.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.4371 Å2 / ksol: 0.342852 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→46.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
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Xplor file |
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