+Open data
-Basic information
Entry | Database: PDB / ID: 4bvk | ||||||
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Title | Structure of Y190E mutant of PhaZ7 PHB depolymerase | ||||||
Components | PHB DEPOLYMERASE PHAZ7 | ||||||
Keywords | HYDROLASE / CATALYTIC TRIAD / BIOPOLYMER BINDING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PAUCIMONAS LEMOIGNEI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.606 Å | ||||||
Authors | Hermawan, S. / Subedi, B. / Papageorgiou, A.C. / Jendrossek, D. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2013 Title: Biochemical Analysis and Structure Determination of Paucimonas Lemoignei Poly(3-Hydroxybutyrate) (Phb) Depolymerase Phaz7 Muteins Reveal the Phb Binding Site and Details of Substrate-Enzyme Interactions. Authors: Jendrossek, D. / Hermawan, S. / Subedi, B. / Papageorgiou, A.C. #1: Journal: J.Mol.Biol. / Year: 2008 Title: Structural Basis of Poly(3-Hydroxybutyrate) Hydrolysis by Phaz7 Depolymerase from Paucimonas Lemoignei. Authors: Papageorgiou, A.C. / Hermawan, S. / Singh, C.B. / Jendrossek, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bvk.cif.gz | 158.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bvk.ent.gz | 124.7 KB | Display | PDB format |
PDBx/mmJSON format | 4bvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/4bvk ftp://data.pdbj.org/pub/pdb/validation_reports/bv/4bvk | HTTPS FTP |
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-Related structure data
Related structure data | 4brsSC 4btvC 4bvjC 4bvlC 4bymC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36445.176 Da / Num. of mol.: 2 / Fragment: RESIDUES 39-380 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PAUCIMONAS LEMOIGNEI (bacteria) / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): WB800 References: UniProt: Q939Q9, poly(3-hydroxybutyrate) depolymerase #2: 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: 2.2 Å3/Da / Density % sol: 43 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5 Details: VAPOUR DIFFUSION HANGING DROP. PROTEIN CONCENTRATION 10 MG/ML. 0.1 M NAOAC (PH 5.0), 0.2 M MGCL2, 18% W/V PEG6000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD / Date: Nov 19, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8123 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→19.8 Å / Num. obs: 81143 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 10.84 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.61→1.66 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4.7 / % possible all: 85.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BRS Resolution: 1.606→19.776 Å / SU ML: 0.14 / σ(F): 2 / Phase error: 15.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.5 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.606→19.776 Å
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Refine LS restraints |
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LS refinement shell |
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