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- PDB-9byu: Structure and stability of an apo thermophilic esterase that hydr... -

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Basic information

Entry
Database: PDB / ID: 9byu
TitleStructure and stability of an apo thermophilic esterase that hydrolyzes polyhydroxybutyrate
ComponentsEsterase, PHB depolymerase family
KeywordsBIOSYNTHETIC PROTEIN / bioplastic / enzymology / polyhydroxyalkanoates / polymer hydrolysis / thermophile / Polyhydroxybutyrate Depolymerase
Function / homologyEsterase, PHB depolymerase / Esterase PHB depolymerase / : / Alpha/Beta hydrolase fold / hydrolase activity / extracellular region / metal ion binding / Esterase, PHB depolymerase family
Function and homology information
Biological speciesLihuaxuella thermophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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) United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: Structure and stability of an apo thermophilic esterase that hydrolyzes polyhydroxybutyrate.
Authors: Thomas, G.M. / Quirk, S. / Lieberman, R.L.
History
DepositionMay 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)32,5883
Polymers32,4421
Non-polymers1462
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.585, 88.585, 49.817
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-553-

HOH

21A-737-

HOH

31A-747-

HOH

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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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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 % sol: 29.28 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion / Details: 120 mM MgCl2, 60 mM Tris, 14% PEG 4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 18, 2023
RadiationMonochromator: Si filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→76.72 Å / Num. obs: 20114 / % possible obs: 89.02 % / Redundancy: 7.2 % / Biso Wilson estimate: 16.75 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 18.03
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.1528 / Num. unique obs: 819 / CC1/2: 0.964

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→76.72 Å / SU ML: 0.1927 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 18.8669
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1932 1985 9.87 %
Rwork0.1405 18125 -
obs0.1458 20110 89.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.6 Å2
Refinement stepCycle: LAST / Resolution: 1.75→76.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2263 0 9 261 2533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00832428
X-RAY DIFFRACTIONf_angle_d0.86823326
X-RAY DIFFRACTIONf_chiral_restr0.0584342
X-RAY DIFFRACTIONf_plane_restr0.0082453
X-RAY DIFFRACTIONf_dihedral_angle_d6.263359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.3537500.285460X-RAY DIFFRACTION32.26
1.79-1.840.3273870.2251781X-RAY DIFFRACTION53.61
1.84-1.90.26661200.19291082X-RAY DIFFRACTION75.55
1.9-1.960.26411300.1581269X-RAY DIFFRACTION86.84
1.96-2.030.21911530.15661376X-RAY DIFFRACTION96.59
2.03-2.110.23181590.15031458X-RAY DIFFRACTION99.75
2.11-2.210.19291650.13961438X-RAY DIFFRACTION100
2.21-2.320.20731520.14171463X-RAY DIFFRACTION100
2.32-2.470.18531560.13921461X-RAY DIFFRACTION100
2.47-2.660.19661640.14521436X-RAY DIFFRACTION100
2.66-2.930.19371620.14631463X-RAY DIFFRACTION100
2.93-3.350.19081610.13451465X-RAY DIFFRACTION100
3.35-4.220.15181640.11561461X-RAY DIFFRACTION100
4.22-76.720.16561620.12891512X-RAY DIFFRACTION100

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