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- PDB-4bvk: Structure of Y190E mutant of PhaZ7 PHB depolymerase -

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Basic information

Entry
Database: PDB / ID: 4bvk
TitleStructure of Y190E mutant of PhaZ7 PHB depolymerase
ComponentsPHB DEPOLYMERASE PHAZ7
KeywordsHYDROLASE / CATALYTIC TRIAD / BIOPOLYMER BINDING
Function / homology
Function and homology information


lipase activity / lipid catabolic process
Similarity search - Function
Lipase EstA/Esterase EstB / Lipase (class 2) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPAUCIMONAS LEMOIGNEI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.606 Å
AuthorsHermawan, 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
DepositionJun 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Category: diffrn_source / exptl_crystal_grow
Item: _diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.method
Revision 1.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHB DEPOLYMERASE PHAZ7
B: PHB DEPOLYMERASE PHAZ7


Theoretical massNumber of molelcules
Total (without water)72,8902
Polymers72,8902
Non-polymers00
Water16,141896
1
A: PHB DEPOLYMERASE PHAZ7


Theoretical massNumber of molelcules
Total (without water)36,4451
Polymers36,4451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHB DEPOLYMERASE PHAZ7


Theoretical massNumber of molelcules
Total (without water)36,4451
Polymers36,4451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.410, 199.320, 44.310
Angle α, β, γ (deg.)90.00, 114.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHB DEPOLYMERASE PHAZ7 / PHB DEPOLYMERASE


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 / water


Mass: 18.015 Da / Num. of mol.: 896 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growMethod: 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.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Nov 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BRS

4brs


Resolution: 1.606→19.776 Å / SU ML: 0.14 / σ(F): 2 / Phase error: 15.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1701 4058 5 %
Rwork0.1348 --
obs0.1366 81141 95.83 %
Solvent computationShrinkage radii: 0.5 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.5 Å2
Refinement stepCycle: LAST / Resolution: 1.606→19.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5080 0 0 896 5976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095285
X-RAY DIFFRACTIONf_angle_d1.187183
X-RAY DIFFRACTIONf_dihedral_angle_d12.7741796
X-RAY DIFFRACTIONf_chiral_restr0.068761
X-RAY DIFFRACTIONf_plane_restr0.006935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.606-1.62490.22331090.18592069X-RAY DIFFRACTION75
1.6249-1.64470.19421410.16982667X-RAY DIFFRACTION94
1.6447-1.66550.2111370.16672611X-RAY DIFFRACTION95
1.6655-1.68740.21531370.16162594X-RAY DIFFRACTION96
1.6874-1.71050.20671400.15472663X-RAY DIFFRACTION95
1.7105-1.73490.18711400.15042663X-RAY DIFFRACTION96
1.7349-1.76080.17771400.14592669X-RAY DIFFRACTION97
1.7608-1.78830.21071400.14362657X-RAY DIFFRACTION95
1.7883-1.81760.21541420.14742690X-RAY DIFFRACTION98
1.8176-1.84890.19211410.14432682X-RAY DIFFRACTION96
1.8489-1.88250.19771420.14162693X-RAY DIFFRACTION97
1.8825-1.91870.16681420.14032707X-RAY DIFFRACTION98
1.9187-1.95790.17451430.13522704X-RAY DIFFRACTION98
1.9579-2.00040.1611420.13242713X-RAY DIFFRACTION98
2.0004-2.04690.17651420.12772684X-RAY DIFFRACTION98
2.0469-2.0980.18851450.13482764X-RAY DIFFRACTION98
2.098-2.15470.15161400.13282664X-RAY DIFFRACTION98
2.1547-2.2180.16521460.12732759X-RAY DIFFRACTION97
2.218-2.28950.15621420.12682715X-RAY DIFFRACTION99
2.2895-2.37120.16861420.12862688X-RAY DIFFRACTION98
2.3712-2.46590.17671450.13152755X-RAY DIFFRACTION97
2.4659-2.57790.15791430.12372718X-RAY DIFFRACTION98
2.5779-2.71350.15951410.12412688X-RAY DIFFRACTION98
2.7135-2.88310.16641430.12322715X-RAY DIFFRACTION97
2.8831-3.10490.15691420.13042697X-RAY DIFFRACTION97
3.1049-3.41590.1761410.13462679X-RAY DIFFRACTION96
3.4159-3.90690.15681390.11842639X-RAY DIFFRACTION95
3.9069-4.90980.1251370.11852599X-RAY DIFFRACTION93
4.9098-19.77770.18331340.16542537X-RAY DIFFRACTION90

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