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Open data
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Basic information
Entry | Database: PDB / ID: 4bvk | ||||||
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Title | Structure of Y190E mutant of PhaZ7 PHB depolymerase | ||||||
![]() | PHB DEPOLYMERASE PHAZ7 | ||||||
![]() | HYDROLASE / CATALYTIC TRIAD / BIOPOLYMER BINDING | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hermawan, S. / Subedi, B. / Papageorgiou, A.C. / Jendrossek, D. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158.6 KB | Display | ![]() |
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PDB format | ![]() | 124.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.3 KB | Display | ![]() |
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Full document | ![]() | 424.5 KB | Display | |
Data in XML | ![]() | 34.7 KB | Display | |
Data in CIF | ![]() | 54.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4brsSC ![]() 4btvC ![]() 4bvjC ![]() 4bvlC ![]() 4bymC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() References: UniProt: Q939Q9, poly(3-hydroxybutyrate) depolymerase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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