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- PDB-8daj: Structure and Biochemistry of a Promiscuous Thermophilic Polyhydr... -

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Basic information

Entry
Database: PDB / ID: 8daj
TitleStructure and Biochemistry of a Promiscuous Thermophilic Polyhydroxybutyrate Depolymerase from Lihuaxuella thermophilia
ComponentsEsterase, PHB depolymerase family
KeywordsBIOSYNTHETIC PROTEIN / Bioplastic / Thermophile / Enzyme / polyhydroxyalkanoates
Function / homology
Function and homology information


hydrolase activity / extracellular region
Similarity search - Function
Esterase, PHB depolymerase / Esterase PHB depolymerase / : / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Esterase, PHB depolymerase family
Similarity search - Component
Biological speciesLihuaxuella thermophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.2 Å
AuthorsThomas, G.M. / Quirk, S. / Huard, D.J.E. / Lieberman, R.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1817796 United States
Citation
Journal: Protein Sci. / Year: 2022
Title: Bioplastic degradation by a polyhydroxybutyrate depolymerase from a thermophilic soil bacterium.
Authors: Thomas, G.M. / Quirk, S. / Huard, D.J.E. / Lieberman, R.L.
#1: Journal: To Be Published
Title: Structure and Biochemistry of a Promiscuous Thermophilic Polyhydroxybutyrate Depolymerase from Lihuaxuella thermophilia
Authors: Thomas, G.M. / Quirk, S. / Huard, D.J.E. / Lieberman, R.L.
History
DepositionJun 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Esterase, PHB depolymerase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,30315
Polymers32,4421
Non-polymers86114
Water6,017334
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.510, 45.510, 211.260
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-406-

IPA

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Components

#1: Protein Esterase, PHB depolymerase family / Polyhydroxybutyrate Depolymerase


Mass: 32441.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lihuaxuella thermophila (bacteria) / Gene: SAMN05444955_11823 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1H8IKU3
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.95 Å3/Da / Density % sol: 36.82 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M citrate pH 5.6, 18% propanol, and 20% PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→36.93 Å / % possible obs: 97.69 % / Redundancy: 16.7 % / Biso Wilson estimate: 11.43 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1339 / Rpim(I) all: 0.03208 / Rrim(I) all: 0.1378 / Net I/σ(I): 11.84
Reflection shellResolution: 1.2→1.243 Å / Redundancy: 6 % / Rmerge(I) obs: 0.4728 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 6485 / CC1/2: 0.824 / CC star: 0.951 / Rpim(I) all: 0.1991 / Rrim(I) all: 0.5169 / % possible all: 81.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.2→36.93 Å / SU ML: 0.1227 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.3247
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1772 3802 2.56 %
Rwork0.1633 144829 -
obs0.1637 148631 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.57 Å2
Refinement stepCycle: LAST / Resolution: 1.2→36.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2278 0 56 334 2668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542506
X-RAY DIFFRACTIONf_angle_d0.96083410
X-RAY DIFFRACTIONf_chiral_restr0.1089348
X-RAY DIFFRACTIONf_plane_restr0.0076464
X-RAY DIFFRACTIONf_dihedral_angle_d6.3713370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.3645740.31652647X-RAY DIFFRACTION48.15
1.22-1.230.31091240.26255062X-RAY DIFFRACTION89.72
1.23-1.250.21921360.22995044X-RAY DIFFRACTION93.33
1.25-1.270.24781360.22665332X-RAY DIFFRACTION95.18
1.27-1.280.20851340.21845267X-RAY DIFFRACTION96.76
1.28-1.30.19341410.20455530X-RAY DIFFRACTION98.57
1.3-1.330.20171340.19435477X-RAY DIFFRACTION99.68
1.33-1.350.20391360.1875527X-RAY DIFFRACTION100
1.35-1.370.23031420.19035556X-RAY DIFFRACTION100
1.37-1.40.21581400.18565553X-RAY DIFFRACTION100
1.4-1.430.1991470.1825537X-RAY DIFFRACTION100
1.43-1.460.20851380.18145475X-RAY DIFFRACTION100
1.46-1.490.25561460.17995526X-RAY DIFFRACTION100
1.49-1.530.20021500.17785483X-RAY DIFFRACTION100
1.53-1.570.22431460.1665593X-RAY DIFFRACTION100
1.57-1.620.16841460.16725497X-RAY DIFFRACTION99.84
1.62-1.670.17141520.16585509X-RAY DIFFRACTION99.98
1.67-1.730.15091500.15885480X-RAY DIFFRACTION99.98
1.73-1.80.14261420.15535587X-RAY DIFFRACTION99.98
1.8-1.880.19351500.1685529X-RAY DIFFRACTION100
1.88-1.980.17961420.15755570X-RAY DIFFRACTION99.98
1.98-2.110.15921440.15345440X-RAY DIFFRACTION100
2.11-2.270.14561500.14795575X-RAY DIFFRACTION99.86
2.27-2.50.19021410.15495457X-RAY DIFFRACTION99.98
2.5-2.860.17561580.15975564X-RAY DIFFRACTION99.93
2.86-3.60.14331520.14815484X-RAY DIFFRACTION100
3.6-36.930.16271510.14085528X-RAY DIFFRACTION99.79

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