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Open data
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Basic information
Entry | Database: PDB / ID: 5j85 | |||||||||
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Title | Ser480Ala mutant of L-arabinonate dehydratase | |||||||||
![]() | Dihydroxyacid dehydratase/phosphogluconate dehydratase | |||||||||
![]() | 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![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rahman, M.M. / Rouvinen, J. / Hakulinen, N. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.3 KB | Display | ![]() |
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PDB format | ![]() | 99.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.7 KB | Display | ![]() |
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Full document | ![]() | 452.6 KB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 34 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5j83C ![]() 5j84C ![]() 2gp4S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() Gene: Rleg9DRAFT_6269 / Plasmid: pBAT4 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-FES / ![]() Source method: isolated from a genetically manipulated source Formula: Fe2S2 / Details: Gram-negative bacteria Source: (gene. exp.) ![]() Gene: 6981653 / Plasmid: pBAT4 / Production host: ![]() ![]() |
#3: Chemical | ChemComp-MG / ![]() Source method: isolated from a genetically manipulated source Formula: Mg / Details: Gram-negative bacteria Source: (gene. exp.) ![]() Gene: 6981653 / Plasmid: pBAT4 / Production host: ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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