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Yorodumi- PDB-3i23: Crystal Structure of an Oxidoreductase (Gfo/Idh/MocA family) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i23 | ||||||
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Title | Crystal Structure of an Oxidoreductase (Gfo/Idh/MocA family) from Enterococcus faecalis. Northeast Structural Genomics Consortium target id EfR167 | ||||||
Components | Oxidoreductase, Gfo/Idh/MocA family | ||||||
Keywords | OXIDOREDUCTASE / Gfo/Idh/MocA family / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Seetharaman, J. / Su, M. / Forouhar, F. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Acton, T.B. / Rost, B. / Montelione, G.T. ...Seetharaman, J. / Su, M. / Forouhar, F. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of an Oxidoreductase (Gfo/Idh/MocA family) from Enterococcus faecalis. Northeast Structural Genomics Consortium target id EfR167 Authors: Seetharaman, J. / Su, M. / Forouhar, F. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Acton, T.B. / Rost, 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 | 3i23.cif.gz | 143.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i23.ent.gz | 119.4 KB | Display | PDB format |
PDBx/mmJSON format | 3i23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/3i23 ftp://data.pdbj.org/pub/pdb/validation_reports/i2/3i23 | 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: 39810.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: EF_1244 / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q835X4 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.31 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MgAcetate 200 mM, CacAcid Ph6.5,PEG8K, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 25, 2009 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 75646 / Num. obs: 75646 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.062 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 4 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 18 / Num. unique all: 3802 / Rsym value: 0.277 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→29.87 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 65514.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.3109 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 28.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.87 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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