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Yorodumi- PDB-3dqp: Crystal structure of the oxidoreductase ylbE from Lactococcus lac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dqp | ||||||
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Title | Crystal structure of the oxidoreductase ylbE from Lactococcus lactis, Northeast Structural Genomics Consortium Target KR121. | ||||||
Components | Oxidoreductase ylbE | ||||||
Keywords | OXIDOREDUCTASE / alpha-beta protein. / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
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 / Oxidoreductase Function and homology information | ||||||
Biological species | Lactococcus lactis subsp. lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å | ||||||
Authors | Forouhar, F. / Neely, H. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Lee, D. / Everett, J.K. / Acton, T.B. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Lee, D. / Everett, J.K. / 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 oxidoreductase ylbE from Lactococcus lactis, Northeast Structural Genomics Consortium Target KR121. Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Lee, D. / Everett, J.K. / B Acton, T. / 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 | 3dqp.cif.gz | 61.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dqp.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 3dqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dqp_validation.pdf.gz | 417.2 KB | Display | wwPDB validaton report |
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Full document | 3dqp_full_validation.pdf.gz | 419.2 KB | Display | |
Data in XML | 3dqp_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 3dqp_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/3dqp ftp://data.pdbj.org/pub/pdb/validation_reports/dq/3dqp | HTTPS FTP |
-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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Details | authors state that the biological unit is possibly dimer. |
-Components
#1: Protein | Mass: 24523.037 Da / Num. of mol.: 1 / Mutation: I64M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria) Strain: IL1403 / Gene: ylbE, LL1109, L119, L119013 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9CGI7 |
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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: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 291 K / Method: microbatch, under oil / pH: 7.5 Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 0.1M HEPES (pH 7.5), 40% PEG 20K, and 0.1M NaMolybdate., microbatch, under oil, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97862 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 2, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97862 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. all: 87349 / Num. obs: 78964 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.054 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 4.59 / Num. unique all: 8724 / Rsym value: 0.18 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.4→9.84 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 852247.64 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.3821 Å2 / ksol: 0.45 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→9.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.45 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
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