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- PDB-7eoa: HR-PETase from Bacterium HR29 -

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Basic information

Entry
Database: PDB / ID: 7eoa
TitleHR-PETase from Bacterium HR29
ComponentsPoly(Ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PETase
Function / homologyAlpha/beta hydrolase fold-5 / Alpha/beta hydrolase family / poly(ethylene terephthalate) hydrolase / Alpha/Beta hydrolase fold / hydrolase activity / ETHANOL / Poly(Ethylene terephthalate) hydrolase
Function and homology information
Biological speciesbacterium HR29 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsWang, J. / Wang, Y.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31725022 China
CitationJournal: To Be Published
Title: Crystal structure of Bomgl, a monoacylglycerol lipase from marine Bacillus
Authors: Wang, Y.H. / Wang, J. / Lan, D.M.
History
DepositionApr 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly(Ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0363
Polymers27,9441
Non-polymers922
Water7,026390
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint3 kcal/mol
Surface area10090 Å2
Unit cell
Length a, b, c (Å)52.490, 52.490, 197.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Poly(Ethylene terephthalate) hydrolase


Mass: 27944.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) bacterium HR29 (bacteria) / Gene: HRbin29_00073 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2H5Z9R5, poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris-HCl pH 8.4, ethanol 19.5% (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.24→27.84 Å / Num. obs: 78799 / % possible obs: 99.29 % / Redundancy: 19.3 % / Biso Wilson estimate: 15.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.01 / Rrim(I) all: 0.048 / Net I/σ(I): 30.8
Reflection shellResolution: 1.24→1.27 Å / Rmerge(I) obs: 0.428 / Num. unique obs: 5427 / CC1/2: 0.908 / Rpim(I) all: 0.223 / Rrim(I) all: 0.428

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EB0

4eb0


Resolution: 1.24→20.52 Å / SU ML: 0.0982 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.6031
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1866 3923 4.98 %
Rwork0.1677 74846 -
obs0.1687 78769 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.53 Å2
Refinement stepCycle: LAST / Resolution: 1.24→20.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1971 0 6 390 2367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532028
X-RAY DIFFRACTIONf_angle_d0.89712775
X-RAY DIFFRACTIONf_chiral_restr0.0778315
X-RAY DIFFRACTIONf_plane_restr0.0076363
X-RAY DIFFRACTIONf_dihedral_angle_d6.3054284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.260.26071090.26642444X-RAY DIFFRACTION92.3
1.26-1.270.23821220.25232542X-RAY DIFFRACTION96.03
1.27-1.290.25191250.22352617X-RAY DIFFRACTION98.14
1.29-1.310.29361250.2752571X-RAY DIFFRACTION96.8
1.31-1.320.23981600.1952599X-RAY DIFFRACTION99.21
1.32-1.340.19911320.18742636X-RAY DIFFRACTION99.53
1.34-1.360.20311300.18662645X-RAY DIFFRACTION99.82
1.36-1.390.18151530.17792652X-RAY DIFFRACTION99.89
1.39-1.410.21841380.16682632X-RAY DIFFRACTION100
1.41-1.440.19981480.16892629X-RAY DIFFRACTION99.96
1.44-1.460.17961450.17212672X-RAY DIFFRACTION99.89
1.46-1.490.21571400.16952651X-RAY DIFFRACTION99.89
1.49-1.530.17991390.16622654X-RAY DIFFRACTION100
1.53-1.560.17741550.16732661X-RAY DIFFRACTION100
1.56-1.60.18241470.1632658X-RAY DIFFRACTION100
1.6-1.640.18991300.17062701X-RAY DIFFRACTION99.96
1.64-1.690.19721200.17022704X-RAY DIFFRACTION100
1.69-1.750.1871260.16742672X-RAY DIFFRACTION100
1.75-1.810.18981510.17172686X-RAY DIFFRACTION100
1.81-1.880.18231510.16342674X-RAY DIFFRACTION100
1.88-1.970.17471310.16972697X-RAY DIFFRACTION99.93
1.97-2.070.16541460.16452694X-RAY DIFFRACTION100
2.07-2.20.18871620.16612721X-RAY DIFFRACTION100
2.2-2.370.19851430.16632713X-RAY DIFFRACTION100
2.37-2.610.16571390.17192749X-RAY DIFFRACTION100
2.61-2.990.19331550.17492759X-RAY DIFFRACTION100
2.99-3.760.15681440.15642840X-RAY DIFFRACTION100
3.76-20.520.20121570.15292973X-RAY DIFFRACTION99.49

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