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Yorodumi- PDB-3qz6: The crystal structure of HpcH/HpaI aldolase from Desulfitobacteri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qz6 | ||||||
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Title | The crystal structure of HpcH/HpaI aldolase from Desulfitobacterium hafniense DCB-2 | ||||||
Components | HpcH/HpaI aldolase | ||||||
Keywords | LYASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG / cytoplasmic | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfitobacterium hafniense (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.999 Å | ||||||
Authors | Tan, K. / Chhor, G. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of HpcH/HpaI aldolase from Desulfitobacterium hafniense DCB-2 Authors: Tan, K. / Chhor, G. / Clancy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qz6.cif.gz | 113 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qz6.ent.gz | 92.9 KB | Display | PDB format |
PDBx/mmJSON format | 3qz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qz/3qz6 ftp://data.pdbj.org/pub/pdb/validation_reports/qz/3qz6 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29090.256 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfitobacterium hafniense (bacteria) Strain: DCB-2 / Gene: Dhaf_2073 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B8FRX2 |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Sodium citrate, 0.1M Tris.HCl, 15% (v/v) PEG400, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2010 / Details: Mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2→44 Å / Num. all: 39752 / Num. obs: 39752 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.773 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 0.773 / Num. unique all: 1931 / Rsym value: 0.016 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.999→43.828 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 16.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.947 Å2 / ksol: 0.344 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.999→43.828 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 16.2071 Å / Origin y: 11.587 Å / Origin z: 17.1328 Å
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Refinement TLS group | Selection details: chain A |