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Yorodumi- PDB-2vss: Wild-type Hydroxycinnamoyl-CoA hydratase lyase in complex with ac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vss | ||||||
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Title | Wild-type Hydroxycinnamoyl-CoA hydratase lyase in complex with acetyl- CoA and vanillin | ||||||
Components | (P-HYDROXYCINNAMOYL COA ...) x 3 | ||||||
Keywords | LYASE / ALDOLASE / CROTONASE / HYDRATASE | ||||||
Function / homology | Function and homology information feruloyl-CoA hydratase/lyase / : / feruloyl-CoA hydratase/lyase activity / isoprenoid catabolic process Similarity search - Function | ||||||
Biological species | PSEUDOMONAS FLUORESCENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å | ||||||
Authors | Bennett, J.P. / Bertin, L.M. / Brzozowski, A.M. / Walton, N.J. / Grogan, G. | ||||||
Citation | Journal: Biochem.J. / Year: 2008 Title: A Ternary Complex of Hydroxycinnamoyl-Coa Hydratase-Lyase (Hchl) with Acetyl-Coa and Vanillin Gives Insights Into Substrate Specificity and Mechanism. Authors: Bennett, J.P. / Bertin, L.M. / Moulton, B. / Fairlamb, I.J.S. / Brzozowski, A.M. / Walton, N.J. / Grogan, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vss.cif.gz | 300.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vss.ent.gz | 242.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vss_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2vss_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2vss_validation.xml.gz | 57.6 KB | Display | |
Data in CIF | 2vss_validation.cif.gz | 77.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/2vss ftp://data.pdbj.org/pub/pdb/validation_reports/vs/2vss | HTTPS FTP |
-Related structure data
Related structure data | 2vsuC 2j5iS S: Starting model for refinement C: citing same article (ref.) |
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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
-P-HYDROXYCINNAMOYL COA ... , 3 types, 6 molecules ABCDEF
#1: Protein | Mass: 31044.613 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Strain: AN103 / Description: INSTITUTE OF FOOD RESEARCH, NORWICH U.K. / Plasmid: YSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69762, trans-feruloyl-CoA hydratase #2: Protein | | Mass: 31021.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Strain: AN103 / Description: INSTITUTE OF FOOD RESEARCH, NORWICH U.K. / Plasmid: YSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69762, trans-feruloyl-CoA hydratase #3: Protein | | Mass: 31072.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Strain: AN103 / Description: INSTITUTE OF FOOD RESEARCH, NORWICH U.K. / Plasmid: YSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69762, trans-feruloyl-CoA hydratase |
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-Non-polymers , 3 types, 321 molecules
#4: Chemical | ChemComp-ACO / #5: Chemical | ChemComp-V55 / | #6: 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: 2.3 Å3/Da / Density % sol: 46.4 % / Description: NONE |
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Crystal grow | Details: PROTEIN CONCENTRATION OF 10 MG ML-1 IN 11% (W/V) PEG 20 000 DA WITH 8% (V/V) PEG 550 DA MONOMETHYL ETHER, 0.8 M SODIUM FORMATE AND 0.2% (V/V) BUTANE 1,4-DIOL IN 0.05 M 2-(N-MORPHOLINO) ...Details: PROTEIN CONCENTRATION OF 10 MG ML-1 IN 11% (W/V) PEG 20 000 DA WITH 8% (V/V) PEG 550 DA MONOMETHYL ETHER, 0.8 M SODIUM FORMATE AND 0.2% (V/V) BUTANE 1,4-DIOL IN 0.05 M 2-(N-MORPHOLINO)ETHANESULFONIC ACID BUFFER PH 5.6. 10MM FERULOYL-COA |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 |
Detector | Date: Aug 6, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→97.13 Å / Num. obs: 73967 / % possible obs: 91.5 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.22→2.27 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.9 / % possible all: 50.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J5I Resolution: 2.22→97.13 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.102 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.226 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.85 Å2
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Refinement step | Cycle: LAST / Resolution: 2.22→97.13 Å
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Refine LS restraints |
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