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- PDB-1sef: Crystal structure of cupin domain protein EF2996 from Enterococcu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1sef | ||||||
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Title | Crystal structure of cupin domain protein EF2996 from Enterococcus faecalis | ||||||
![]() | conserved hypothetical protein | ||||||
![]() | structural genomics / unknown function / NYSGXRC target T1582 / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | ![]() (S)-ureidoglycine aminohydrolase / (S)-ureidoglycine aminohydrolase, cupin domain / EutQ-like cupin domain / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fedorov, A.A. / Fedorov, E.V. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: The crystal structure of conserved hypothetical protein from Enterococcus Faecalis V583 Authors: Fedorov, A.A. / Fedorov, E.V. / Almo, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.9 KB | Display | ![]() |
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PDB format | ![]() | 47.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.1 KB | Display | ![]() |
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Full document | ![]() | 442.4 KB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 18.5 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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Unit cell |
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Details | The biological assembly is a monomer |
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Components
#1: Protein | Mass: 31040.646 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The conserved hypothetical protein with unknown function Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.549 Å3/Da / Density % sol: 63.92 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: MPD, calcium chloride, bis-Tris , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 16, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.01 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→25 Å / Num. all: 27665 / Num. obs: 27665 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.052 / Net I/σ(I): 39.6 |
Reflection shell | Resolution: 2.05→2.12 Å / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 9.2 / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.7649 Å2 / ksol: 0.36885 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→25 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.05 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
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Xplor file |
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