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Yorodumi- PDB-4hch: CRYSTAL STRUCTURE OF D-GLUCARATE DEHYDRATASE FROM AGROBACTERIUM T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hch | |||||||||
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Title | CRYSTAL STRUCTURE OF D-GLUCARATE DEHYDRATASE FROM AGROBACTERIUM TUMEFACIENS complexed with magnesium and L-tartrate | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.699 Å | |||||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Sakai, A. / Gerlt, J.A. / Almo, S.C. | |||||||||
Citation | Journal: To be Published Title: CRYSTAL STRUCTURE OF D-GLUCARATE DEHYDRATASE FROM AGROBACTERIUM TUMEFACIENS complexed with magnesium and L-tartrate Authors: Fedorov, A.A. / Fedorov, E.V. / Sakai, A. / 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 | 4hch.cif.gz | 190.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hch.ent.gz | 147.2 KB | Display | PDB format |
PDBx/mmJSON format | 4hch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/4hch ftp://data.pdbj.org/pub/pdb/validation_reports/hc/4hch | HTTPS FTP |
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-Related structure data
Related structure data | 1rvkS 4hcm S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45133.969 Da / Num. of mol.: 2 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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-Non-polymers , 7 types, 970 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | ChemComp-PGE / | #7: Chemical | ChemComp-EDO / #8: 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: 2.58 Å3/Da / Density % sol: 52.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG3350, 0.2M POTASSIUM SODIUM TARTRATE TETRAHYDRATE, pH 7.0, 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: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2008 |
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: 1.699→37.793 Å / Num. all: 98528 / Num. obs: 98528 / % possible obs: 98.27 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RVK Resolution: 1.699→37.793 Å / SU ML: 0.14 / σ(F): 0 / Phase error: 16.88 / 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: 1.699→37.793 Å
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Refine LS restraints |
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LS refinement shell |
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