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Yorodumi- PDB-3ew7: Crystal structure of the Lmo0794 protein from Listeria monocytoge... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ew7 | ||||||
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Title | Crystal structure of the Lmo0794 protein from Listeria monocytogenes. Northeast Structural Genomics Consortium target LmR162. | ||||||
Components | Lmo0794 protein | ||||||
Keywords | structural genomics / unknown function / Q8Y8U8_LISMO / Lmo0794 / putative NAD-dependent Epimerase/dehydratase / LmR162 / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | NAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Lmo0794 protein Function and homology information | ||||||
Biological species | Listeria monocytogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.73 Å | ||||||
Authors | Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Wang, D. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Wang, D. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the Lmo0794 protein from Listeria monocytogenes. Authors: Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Wang, D. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ew7.cif.gz | 47.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ew7.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ew7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/3ew7 ftp://data.pdbj.org/pub/pdb/validation_reports/ew/3ew7 | 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24563.934 Da / Num. of mol.: 1 / Mutation: I71V, K142R, H207R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: ATCC BAA-679/EGD-e/Serovar 1/2a / Gene: lmo0794 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: Q8Y8U8 |
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#2: 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: 3.8 Å3/Da / Density % sol: 67.65 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 18% PEG 4000, 0.1M KH(2)PO(4), 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97894, 0.97926, 0.96785 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 8, 2008 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.73→50 Å / Num. all: 19317 / Num. obs: 19111 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 16.05 | ||||||||||||
Reflection shell | Resolution: 2.73→2.85 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 4.05 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.73→33.76 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 362304.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.7195 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.73→33.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.73→2.9 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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