+Open data
-Basic information
Entry | Database: PDB / ID: 5j84 | |||||||||
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Title | Crystal structure of L-arabinonate dehydratase in holo-form | |||||||||
Components | Dihydroxy-acid dehydratase | |||||||||
Keywords | LYASE / L-arabinonate dehydratase / L-arabonate dehydratase / pentonate dehydratase / 2Fe2S cluster | |||||||||
Function / homology | Function and homology information L-arabinonate dehydratase / D-fuconate dehydratase / D-fuconate dehydratase activity / L-arabinonate dehydratase activity / galactonate dehydratase / galactonate dehydratase activity / arabinose catabolic process / 2 iron, 2 sulfur cluster binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Rhizobium leguminosarum bv. trifolii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 | 5j84.cif.gz | 884.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j84.ent.gz | 736.8 KB | Display | PDB format |
PDBx/mmJSON format | 5j84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j84_validation.pdf.gz | 513.6 KB | Display | wwPDB validaton report |
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Full document | 5j84_full_validation.pdf.gz | 546.6 KB | Display | |
Data in XML | 5j84_validation.xml.gz | 168 KB | Display | |
Data in CIF | 5j84_validation.cif.gz | 234.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/5j84 ftp://data.pdbj.org/pub/pdb/validation_reports/j8/5j84 | HTTPS FTP |
-Related structure data
Related structure data | 5j83C 5j85C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 63858.938 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: Gram-negative bacteria Source: (gene. exp.) Rhizobium leguminosarum bv. trifolii (strain WSM2304) (bacteria) Strain: WSM2304 / Gene: Rleg2_2909 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5ZZ34, dihydroxy-acid dehydratase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-FES / #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: 3.2 Å3/Da / Density % sol: 62 % / Description: 3D-Plate |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 4 M Sodium formate, 0.1 M MES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.97957 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2012 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97957 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. obs: 246940 / % possible obs: 99.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 43 Å2 / CC1/2: 0.995 / Rsym value: 0.091 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GP4 Resolution: 2.4→39.889 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.35
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→39.889 Å
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Refine LS restraints |
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LS refinement shell |
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