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Open data
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Basic information
Entry | Database: PDB / ID: 4bvj | ||||||
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Title | Structure of Y105A 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 | ![]() | 168 KB | Display | ![]() |
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PDB format | ![]() | 131.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431 KB | Display | ![]() |
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Full document | ![]() | 433.8 KB | Display | |
Data in XML | ![]() | 37.6 KB | Display | |
Data in CIF | ![]() | 60.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4brsSC ![]() 4btvC ![]() 4bvkC ![]() 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36259.012 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: Chemical | #3: 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 NH4CL, 20% W/V PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / 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→20 Å / Num. obs: 84896 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BRS Resolution: 1.599→20.005 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 18.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.599→20.005 Å
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Refine LS restraints |
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LS refinement shell |
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