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Yorodumi- PDB-3oid: Crystal Structure of Enoyl-ACP Reductases III (FabL) from B. subt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oid | ||||||
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Title | Crystal Structure of Enoyl-ACP Reductases III (FabL) from B. subtilis (complex with NADP and TCL) | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADPH] | ||||||
Keywords | OXIDOREDUCTASE / Fatty acid synthesis / Enoyl-ACP Reductases / FabL / Rossmann-like fold / NADPH binding | ||||||
Function / homology | Function and homology information enoyl-[acyl-carrier-protein] reductase (NADPH) / fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NADP binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Kim, K.-H. / Ha, B.H. / Kim, S.J. / Hong, S.K. / Hwang, K.Y. / Kim, E.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Crystal Structures of Enoyl-ACP Reductases I (FabI) and III (FabL) from B. subtilis Authors: Kim, K.-H. / Ha, B.H. / Kim, S.J. / Hong, S.K. / Hwang, K.Y. / Kim, E.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oid.cif.gz | 215.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oid.ent.gz | 172.5 KB | Display | PDB format |
PDBx/mmJSON format | 3oid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oid_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 3oid_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 3oid_validation.xml.gz | 45.4 KB | Display | |
Data in CIF | 3oid_validation.cif.gz | 62.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/3oid ftp://data.pdbj.org/pub/pdb/validation_reports/oi/3oid | HTTPS FTP |
-Related structure data
Related structure data | 3oicSC 3oifC 3oigC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28281.445 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: FabL / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P71079, EC: 1.3.1.10 #2: Chemical | ChemComp-TCL / #3: Chemical | ChemComp-NDP / #4: 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: 2.43 Å3/Da / Density % sol: 49.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.6M sodium citrate , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 14, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 100171 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 34.7 / Num. measured all: 1861429 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 8.95 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3OIC Resolution: 1.8→36.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.797 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.994 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→36.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.799→1.846 Å / Total num. of bins used: 20
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