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Yorodumi- PDB-2j5s: Structural of ABDH, a beta-diketone hydrolase from the Cyanobacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j5s | ||||||
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Title | Structural of ABDH, a beta-diketone hydrolase from the Cyanobacterium Anabaena sp. PCC 7120 bound to (S)-3-oxocyclohexyl acetic acid | ||||||
Components | BETA-DIKETONE HYDROLASE | ||||||
Keywords | HYDROLASE / ENZYME EVOLUTION / C-C BOND HYDROLASE / LYASE / CROTONASE / BIOCATALYSIS / BETA-DIKETONE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ANABAENA SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Bennett, J.P. / Whittingham, J.L. / Brzozowski, A.M. / Leonard, P.M. / Grogan, G. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Structural Characterisation of a Beta Diketone Hydrolase from the Cyanobacterium Anabaena Sp. Pcc 7120 in Native and Product Bound Forms, a Coenzyme A-Independent Member of the Crotonase Suprafamily Authors: Bennett, J.P. / Whittingham, J.L. / Brzozowski, A.M. / Leonard, P.M. / Grogan, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j5s.cif.gz | 127.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j5s.ent.gz | 98.5 KB | Display | PDB format |
PDBx/mmJSON format | 2j5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j5s_validation.pdf.gz | 449 KB | Display | wwPDB validaton report |
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Full document | 2j5s_full_validation.pdf.gz | 452.8 KB | Display | |
Data in XML | 2j5s_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 2j5s_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/2j5s ftp://data.pdbj.org/pub/pdb/validation_reports/j5/2j5s | HTTPS FTP |
-Related structure data
Related structure data | 2j5gC 1o8uS 2j5j 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 30067.037 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PROTEIN WAS CO-CRYSTALLISED WITH SUBSTRATE / Source: (gene. exp.) ANABAENA SP. (bacteria) / Strain: PCC 7120 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8YNV6, beta-diketone hydrolase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | SEQUENCE CONTAINS N-TERMINAL CLEAVABLE HIS TAG OF SIX HISTIDINE RESIDUES. | |
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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: 2.04 Å3/Da / Density % sol: 39.61 % |
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Crystal grow | pH: 7.5 Details: 0.1 M BIS-TRIS PROPANE PH 7.5, 20% PEG 3350, 0.2 M SODIUM MALONATE, 0.01 M BICYCLO[2.2.2]OCTANE-2,6-DIONE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 20, 2006 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SILICON (1 1 1) CHANNEL- CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→40.19 Å / Num. obs: 64435 / % possible obs: 98.9 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 32.04 |
Reflection shell | Resolution: 1.57→1.63 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.93 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1O8U Resolution: 1.57→40.19 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.227 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.19 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→40.19 Å
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Refine LS restraints |
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