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Yorodumi- PDB-4ur7: Crystal structure of keto-deoxy-D-galactarate dehydratase complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ur7 | ||||||
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Title | Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with pyruvate | ||||||
Components | KETO-DEOXY-D-GALACTARATE DEHYDRATASE | ||||||
Keywords | LYASE / DECARBOXYLATE / BIOCATALYSIS / OXIDATIVE PATHWAY / D-GALACTURONIC ACID | ||||||
Function / homology | Function and homology information 5-dehydro-4-deoxyglucarate dehydratase / 5-dehydro-4-deoxyglucarate dehydratase activity / D-glucarate catabolic process / 4-hydroxy-tetrahydrodipicolinate synthase activity Similarity search - Function | ||||||
Biological species | AGROBACTERIUM TUMEFACIENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å | ||||||
Authors | Taberman, H. / Parkkinen, T. / Hakulinen, N. / Rouvinen, J. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Structure and Function of a Decarboxylating Agrobacterium Tumefaciens Keto-Deoxy-D-Galactarate Dehydratase. Authors: Taberman, H. / Andberg, M.B. / Parkkinen, T. / Janis, J. / Penttila, M. / Hakulinen, N. / Koivula, A. / Rouvinen, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ur7.cif.gz | 274.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ur7.ent.gz | 222.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ur7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ur7_validation.pdf.gz | 479.1 KB | Display | wwPDB validaton report |
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Full document | 4ur7_full_validation.pdf.gz | 485 KB | Display | |
Data in XML | 4ur7_validation.xml.gz | 60.5 KB | Display | |
Data in CIF | 4ur7_validation.cif.gz | 91.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/4ur7 ftp://data.pdbj.org/pub/pdb/validation_reports/ur/4ur7 | HTTPS FTP |
-Related structure data
Related structure data | 4ur8C 5hwjC 5hwmC 5hwnC 4ur5 C: citing same article (ref.) S: Starting model for refinement |
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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: 33631.402 Da / Num. of mol.: 4 / Fragment: RESIDUES 3-303 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AGROBACTERIUM TUMEFACIENS (bacteria) / Plasmid: PBAT4-ATKDG / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) References: UniProt: Q8UB77, Lyases; Carbon-oxygen lyases; Hydro-lyases #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-FMT / #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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: BICINE PH 8.5, SODIUM FORMATE, PEG MME 5000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2013 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 214991 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.64 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.27 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4UR5 4ur5 Resolution: 1.499→48.087 Å / SU ML: 0.15 / σ(F): 1.36 / Phase error: 19.22 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.68 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.499→48.087 Å
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Refine LS restraints |
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LS refinement shell |
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