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Yorodumi- PDB-8gbb: Short-chain dehydrogenase/reductase (SDR) from multi-drug resista... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gbb | ||||||
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Title | Short-chain dehydrogenase/reductase (SDR) from multi-drug resistant Acinetobacter baumannii | ||||||
Components | SDR family oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / Short chain / SDR / Acinetobacter baumannii | ||||||
Function / homology | 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 / SDR family oxidoreductase Function and homology information | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Shaw, K.I. / Ghafoori, S.M. / Forwood, J.K. | ||||||
Funding support | 1items
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Citation | Journal: Plos One / Year: 2023 Title: Crystallographic structure determination and analysis of a potential short-chain dehydrogenase/reductase (SDR) from multi-drug resistant Acinetobacter baumannii. Authors: Ghafoori, S.M. / Abdollahpour, S. / Shirmast, P. / Forwood, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gbb.cif.gz | 190.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gbb.ent.gz | 152.4 KB | Display | PDB format |
PDBx/mmJSON format | 8gbb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gbb_validation.pdf.gz | 428.7 KB | Display | wwPDB validaton report |
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Full document | 8gbb_full_validation.pdf.gz | 430.9 KB | Display | |
Data in XML | 8gbb_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 8gbb_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/8gbb ftp://data.pdbj.org/pub/pdb/validation_reports/gb/8gbb | HTTPS FTP |
-Related structure data
Related structure data | 2d1yS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 27827.480 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: F4T85_19375, FJU42_12090, HBK86_07635 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0M3FP68 #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: 2.27 Å3/Da / Density % sol: 45.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2 M lithium chloride 0.1 M Tris pH 8.0, 20% (v/v) polyethylene glycol 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→29.4 Å / Num. obs: 20190 / % possible obs: 99.72 % / Redundancy: 28.6 % / Biso Wilson estimate: 24.95 Å2 / CC1/2: 0.89 / Rmerge(I) obs: 0.8597 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 2.4→2.486 Å / Rmerge(I) obs: 2.106 / Mean I/σ(I) obs: 4.67 / Num. unique obs: 1976 / CC1/2: 0.694 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2D1Y Resolution: 2.4→29.4 Å / SU ML: 0.2365 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1326 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→29.4 Å
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Refine LS restraints |
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LS refinement shell |
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