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- PDB-8wdm: Crystal structure of a novel PU plastic degradation enzyme from T... -

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Basic information

Entry
Database: PDB / ID: 8wdm
TitleCrystal structure of a novel PU plastic degradation enzyme from Thermaerobacter marianensis
ComponentsCarboxylic ester hydrolase
KeywordsHYDROLASE / PU plastic / degradation / catalysis
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / cholinesterase activity
Similarity search - Function
: / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Carboxylic ester hydrolase
Similarity search - Component
Biological speciesThermaerobacter marianensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLi, Z.S. / Wang, H. / Gao, J. / Chen, Y.Y. / Wei, H.L. / Li, Q. / Han, X. / Wei, R. / Liu, W.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371530 China
CitationJournal: To Be Published
Title: Crystal structure of a novel PU plastic degradation enzyme from Thermaerobacter marianensis
Authors: Li, Z.S. / Wang, H. / Gao, J. / Chen, Y.Y. / Wei, H.L. / Li, Q. / Han, X. / Wei, R. / Liu, W.D.
History
DepositionSep 15, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxylic ester hydrolase
B: Carboxylic ester hydrolase
C: Carboxylic ester hydrolase
D: Carboxylic ester hydrolase


Theoretical massNumber of molelcules
Total (without water)225,5674
Polymers225,5674
Non-polymers00
Water9,476526
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.879, 81.879, 667.347
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Carboxylic ester hydrolase


Mass: 56391.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermaerobacter marianensis (strain ATCC 700841 / DSM 12885 / JCM 10246 / 7p75a) (bacteria)
Gene: Tmar_0630 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: E6SHQ4, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O

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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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 1M Na+/K+HPO4, pH 7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / Wavelength: 0.979191 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979191 Å / Relative weight: 1
ReflectionResolution: 2.2→48.6 Å / Num. obs: 127917 / % possible obs: 99.9 % / Redundancy: 21.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.314 / Rpim(I) all: 0.069 / Rrim(I) all: 0.321 / Χ2: 0.55 / Net I/σ(I): 8.7 / Num. measured all: 2795185
Reflection shellResolution: 2.2→2.24 Å / % possible obs: 98.5 % / Redundancy: 20.2 % / Rmerge(I) obs: 1.394 / Num. measured all: 127078 / Num. unique obs: 6278 / CC1/2: 0.886 / Rpim(I) all: 0.315 / Rrim(I) all: 1.429 / Χ2: 0.15 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→41.58 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.68 / Phase error: 29.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2652 6356 4.99 %
Rwork0.2313 --
obs0.233 127296 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→41.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14920 0 0 526 15446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.285
X-RAY DIFFRACTIONf_dihedral_angle_d8.3152213
X-RAY DIFFRACTIONf_chiral_restr0.0732255
X-RAY DIFFRACTIONf_plane_restr0.0232831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.280.37656430.35712151X-RAY DIFFRACTION100
2.28-2.370.35646220.309612000X-RAY DIFFRACTION100
2.37-2.480.32676480.283412163X-RAY DIFFRACTION100
2.48-2.610.3146320.273412032X-RAY DIFFRACTION100
2.61-2.770.32176240.279412076X-RAY DIFFRACTION100
2.77-2.990.30786240.267312079X-RAY DIFFRACTION100
2.99-3.290.28856390.249912172X-RAY DIFFRACTION100
3.29-3.760.25066430.222612039X-RAY DIFFRACTION100
3.76-4.740.23776340.201212114X-RAY DIFFRACTION100
4.74-41.580.20636470.181312114X-RAY DIFFRACTION100

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