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- PDB-8xrz: Crystal structure of a novel PU plastic degradation enzyme with l... -

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Basic information

Entry
Database: PDB / ID: 8xrz
TitleCrystal structure of a novel PU plastic degradation enzyme with ligand from Thermaerobacter marianensis
ComponentsCarboxylic ester hydrolase
KeywordsHYDROLASE / PU degradation / ligand / 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: 2.11 Å
AuthorsLi, Z.S. / Wang, H. / Zheng, Z.R. / Cong, L. / Chen, Y.Y. / Han, X. / Wei, R. / Uwe, B. / 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 with ligand from Thermaerobacter marianensis
Authors: Li, Z.S. / Wang, H. / Zheng, Z.R. / Cong, L. / Chen, Y.Y. / Han, X. / Wei, R. / Uwe, B. / liu, W.D.
History
DepositionJan 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 15, 2025Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,9136
Polymers225,5034
Non-polymers4102
Water8,449469
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.566, 81.566, 667.529
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: 56375.660 Da / Num. of mol.: 4 / Mutation: S215A
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-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: Chemical ChemComp-A1D5F / 4-oxidanylbutyl ~{N}-[4-[(4-aminophenyl)methyl]phenyl]carbamate


Mass: 314.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.01 Å3/Da / Density % sol: 59.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 2.6M ,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 143267 / % possible obs: 99.9 % / Redundancy: 33 % / CC1/2: 0.996 / Net I/σ(I): 11.5
Reflection shellResolution: 2.11→2.18 Å / Num. unique obs: 14345 / CC1/2: 0.767

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→48.52 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.962 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22514 7260 5.1 %RANDOM
Rwork0.19088 ---
obs0.19262 136174 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.846 Å2
Baniso -1Baniso -2Baniso -3
1-10.1 Å20 Å20 Å2
2--10.1 Å20 Å2
3----20.19 Å2
Refinement stepCycle: 1 / Resolution: 2.11→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15040 0 5 469 15514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01215460
X-RAY DIFFRACTIONr_bond_other_d0.0020.01614551
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.81921115
X-RAY DIFFRACTIONr_angle_other_deg0.5061.73733215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35251976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.1685188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.771102153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.22257
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219401
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023883
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_it4.3443.8577916
X-RAY DIFFRACTIONr_mcbond_other4.3433.8577916
X-RAY DIFFRACTIONr_mcangle_it5.7386.9319888
X-RAY DIFFRACTIONr_mcangle_other5.7386.9319889
X-RAY DIFFRACTIONr_scbond_it4.1993.9727544
X-RAY DIFFRACTIONr_scbond_other4.1673.9737537
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5257.23511216
X-RAY DIFFRACTIONr_long_range_B_refined7.75246.8467399
X-RAY DIFFRACTIONr_long_range_B_other7.75146.8667263
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.163 Å
RfactorNum. reflection% reflection
Rfree0.295 509 -
Rwork0.207 9986 -
obs--99 %

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