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- PDB-8yma: CRYSTAL STRUCTURE OF A NOVEL PU PLASTIC DEGRADATION ENZYME FROM T... -

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Basic information

Entry
Database: PDB / ID: 8yma
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, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / 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: 2.07 Å
AuthorsLi, Z.S. / Wang, H. / Gao, J. / Chen, Y.Y. / Wei, H.L. / Han, X. / Wei, R. / Bornscheuer, U.T. / Liu, W.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) 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. / Han, X. / Wei, R. / Bornscheuer, U.T. / Liu, W.D.
History
DepositionMar 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)225,6635
Polymers225,5674
Non-polymers961
Water8,629479
1
A: Carboxylic ester hydrolase


Theoretical massNumber of molelcules
Total (without water)56,3921
Polymers56,3921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carboxylic ester hydrolase


Theoretical massNumber of molelcules
Total (without water)56,3921
Polymers56,3921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4882
Polymers56,3921
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Carboxylic ester hydrolase


Theoretical massNumber of molelcules
Total (without water)56,3921
Polymers56,3921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.834, 81.834, 667.371
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
Details: The sequence of organism Thermaerobacter marianensis is not available, replaced by E6SHQ4 temporarily.
Source: (gene. exp.) Thermaerobacter marianensis (bacteria) / Gene: Tmar_0630
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: E6SHQ4, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.03 Å3/Da / Density % sol: 59.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.0M (NH4)2HPO4, 0.1M imidazole pH 8.0, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.07→48.59 Å / Num. obs: 153365 / % possible obs: 99.9 % / Redundancy: 21.5 % / CC1/2: 0.995 / Net I/σ(I): 11.8
Reflection shellResolution: 2.07→2.1 Å / Redundancy: 21.3 % / Num. unique obs: 7533 / CC1/2: 0.643

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→48.59 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.063 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22742 7698 5 %RANDOM
Rwork0.18171 ---
obs0.184 145412 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.772 Å2
Baniso -1Baniso -2Baniso -3
1-11.84 Å20 Å20 Å2
2--11.84 Å20 Å2
3----23.68 Å2
Refinement stepCycle: 1 / Resolution: 2.07→48.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14893 0 5 481 15379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01215311
X-RAY DIFFRACTIONr_bond_other_d0.0010.01614325
X-RAY DIFFRACTIONr_angle_refined_deg1.511.81420931
X-RAY DIFFRACTIONr_angle_other_deg0.5231.73232697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49151977
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.865175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.607102091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.22250
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219202
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023806
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.4075.0667920
X-RAY DIFFRACTIONr_mcbond_other6.4075.0667919
X-RAY DIFFRACTIONr_mcangle_it8.7189.1179893
X-RAY DIFFRACTIONr_mcangle_other8.7189.1179894
X-RAY DIFFRACTIONr_scbond_it5.9645.1837391
X-RAY DIFFRACTIONr_scbond_other5.9625.1837388
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.19.4611033
X-RAY DIFFRACTIONr_long_range_B_refined12.90161.0767633
X-RAY DIFFRACTIONr_long_range_B_other12.89761.1267453
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.121 Å
RfactorNum. reflection% reflection
Rfree0.286 581 -
Rwork0.199 10676 -
obs--98.64 %

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