+Open data
-Basic information
Entry | Database: PDB / ID: 5j85 | |||||||||
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Title | Ser480Ala mutant of L-arabinonate dehydratase | |||||||||
Components | Dihydroxyacid dehydratase/phosphogluconate dehydratase | |||||||||
Keywords | LYASE / L-arabinonate dehydratase / L-arabonate dehydratase / pentonate dehydratase / 2Fe2S cluster | |||||||||
Function / homology | Dihydroxy-acid/6-phosphogluconate dehydratase / IlvD/EDD, N-terminal domain / Dihydroxy-acid dehydratase, C-terminal / Dehydratase family / hydro-lyase activity / FE2/S2 (INORGANIC) CLUSTER / Dihydroxyacid dehydratase/phosphogluconate dehydratase Function and homology information | |||||||||
Biological species | Rhizobium leguminosarum bv. trifolii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Rahman, M.M. / Rouvinen, J. / Hakulinen, N. | |||||||||
Funding support | Finland, 2items
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Citation | Journal: ACS Chem. Biol. / Year: 2017 Title: The Crystal Structure of a Bacterial l-Arabinonate Dehydratase Contains a [2Fe-2S] Cluster. Authors: Rahman, M.M. / Andberg, M. / Thangaraj, S.K. / Parkkinen, T. / Penttila, M. / Janis, J. / Koivula, A. / Rouvinen, J. / Hakulinen, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j85.cif.gz | 129.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j85.ent.gz | 99.3 KB | Display | PDB format |
PDBx/mmJSON format | 5j85.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/5j85 ftp://data.pdbj.org/pub/pdb/validation_reports/j8/5j85 | HTTPS FTP |
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-Related structure data
Related structure data | 5j83C 5j84C 2gp4S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 63842.938 Da / Num. of mol.: 1 / Mutation: S480A Source method: isolated from a genetically manipulated source Details: Gram-negative bacteria Source: (gene. exp.) Rhizobium leguminosarum bv. trifolii (bacteria) Gene: Rleg9DRAFT_6269 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I9XDU6 |
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#2: Chemical | ChemComp-FES / Mass: 175.820 Da / Num. of mol.: 1 / Mutation: S480A Source method: isolated from a genetically manipulated source Formula: Fe2S2 / Details: Gram-negative bacteria Source: (gene. exp.) Rhizobium leguminosarum bv. trifolii (bacteria) Gene: 6981653 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: L-arabinonate dehydratase |
#3: Chemical | ChemComp-MG / Mass: 24.305 Da / Num. of mol.: 1 / Mutation: S480A Source method: isolated from a genetically manipulated source Formula: Mg / Details: Gram-negative bacteria Source: (gene. exp.) Rhizobium leguminosarum bv. trifolii (bacteria) Gene: 6981653 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: L-arabinonate dehydratase |
#4: 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: 5.3 Å3/Da / Density % sol: 77 % / Description: cubic |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.1 M sodium chloride, 0.1 M BTP pH 9.0, 5 mM magnesium chloride, 17% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 42880 / % possible obs: 99.8 % / Redundancy: 9.7 % / Biso Wilson estimate: 74 Å2 / CC1/2: 0.998 / Rsym value: 0.082 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 2.4 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GP4 Resolution: 2.6→38.904 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.46 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→38.904 Å
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Refine LS restraints |
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LS refinement shell |
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