+Open data
-Basic information
Entry | Database: PDB / ID: 7sub | |||||||||
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Title | 3-oxoacyl-ACP reductase FabG | |||||||||
Components | 3-oxoacyl-reductase | |||||||||
Keywords | OXIDOREDUCTASE / Fatty Acid Biosynthesis / Fatty Acid Metabolism | |||||||||
Function / homology | 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / 3-oxoacyl-reductase Function and homology information | |||||||||
Biological species | Syntrophus aciditrophicus SB (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | |||||||||
Authors | Thomas, L.M. / Karr, E.A. / Dinh, D.M. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2023 Title: Crystal structure of a putative 3-hydroxypimelyl-CoA dehydrogenase, Hcd1, from Syntrophus aciditrophicus strain SB at 1.78 A resolution Authors: Dinh, D.M. / Thomas, L.M. / Karr, E.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sub.cif.gz | 72.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sub.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 7sub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sub_validation.pdf.gz | 443 KB | Display | wwPDB validaton report |
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Full document | 7sub_full_validation.pdf.gz | 447.9 KB | Display | |
Data in XML | 7sub_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 7sub_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/su/7sub ftp://data.pdbj.org/pub/pdb/validation_reports/su/7sub | HTTPS FTP |
-Related structure data
Related structure data | 2hq1S 2uvdS 4jroS 4rzhS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28751.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Syntrophus aciditrophicus SB (bacteria) Strain: SB / Gene: SYN_01680 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q2LXS6, 3-oxoacyl-[acyl-carrier-protein] reductase |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.33 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium Malonate pH = 4.0 12% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97922 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2021 / Details: monochrometer |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97922 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→39.2 Å / Num. obs: 24038 / % possible obs: 99.9 % / Redundancy: 9.7 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.017 / Rrim(I) all: 0.04 / Net I/σ(I): 31.1 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1338 / CC1/2: 0.856 / Rpim(I) all: 0.401 / Rrim(I) all: 0.886 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2hq1, 2uvd, 4rzh, 4jro Resolution: 1.78→39.2 Å / SU ML: 0.228 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.1931 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→39.2 Å
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Refine LS restraints |
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LS refinement shell |
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