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Yorodumi- PDB-4hcd: Crystal structure of D-glucarate dehydratase from agrobacterium t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hcd | ||||||
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Title | Crystal structure of D-glucarate dehydratase from agrobacterium tumefaciens complexed with magnesium | ||||||
Components | Isomerase/lactonizing enzyme | ||||||
Keywords | ISOMERASE / Enolase fold / D-GLUCARATE DEHYDRATASE / D-GLUCARATE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Sakai, A. / Millikin, C. / Gerlt, J.A. / Almo, S.C. | ||||||
Citation | Journal: To be Published Title: Crystal structure of D-glucarate dehydratase from agrobacterium tumefaciens complexed with magnesium Authors: Fedorov, A.A. / Fedorov, E.V. / Sakai, A. / Millikin, C. / Gerlt, J.A. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hcd.cif.gz | 102.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hcd.ent.gz | 81.8 KB | Display | PDB format |
PDBx/mmJSON format | 4hcd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/4hcd ftp://data.pdbj.org/pub/pdb/validation_reports/hc/4hcd | HTTPS FTP |
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-Related structure data
Related structure data | 4hcm |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 45696.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / ATCC 33970 / Gene: Atu3453 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CSI0 | ||||||
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#2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | #5: 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: 2.57 Å3/Da / Density % sol: 52.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 3.0M SODIUM CHLORIDE, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 20, 2003 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→24.913 Å / Num. all: 52225 / Num. obs: 52225 / % possible obs: 99.88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→24.913 Å / SU ML: 0.16 / σ(F): 0 / Phase error: 16.66 / 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: 1.7→24.913 Å
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Refine LS restraints |
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LS refinement shell |
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