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- PDB-7xtv: The structure of MHET-bound TfCut S130A -

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Basic information

Entry
Database: PDB / ID: 7xtv
TitleThe structure of MHET-bound TfCut S130A
Componentsalpha/beta hydrolase
KeywordsHYDROLASE / PET hydrolase / PBAT hydrolase / enzyme engineering / cutinase
Function / homologyACETATE ION / 4-(2-hydroxyethyloxycarbonyl)benzoic acid / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsYang, Y. / Jiang, P.C. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870790 China
National Natural Science Foundation of China (NSFC)31971205 China
National Natural Science Foundation of China (NSFC)32101016 China
CitationJournal: Nat Commun / Year: 2023
Title: Complete bio-degradation of poly(butylene adipate-co-terephthalate) via engineered cutinases.
Authors: Yang, Y. / Min, J. / Xue, T. / Jiang, P. / Liu, X. / Peng, R. / Huang, J.W. / Qu, Y. / Li, X. / Ma, N. / Tsai, F.C. / Dai, L. / Zhang, Q. / Liu, Y. / Chen, C.C. / Guo, R.T.
History
DepositionMay 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alpha/beta hydrolase
B: alpha/beta hydrolase
C: alpha/beta hydrolase
D: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,92220
Polymers113,2114
Non-polymers1,71116
Water15,619867
1
A: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7114
Polymers28,3031
Non-polymers4083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7845
Polymers28,3031
Non-polymers4814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7666
Polymers28,3031
Non-polymers4635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6605
Polymers28,3031
Non-polymers3574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.489, 91.489, 247.646
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-511-

HOH

21B-514-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
alpha/beta hydrolase / Cutinase


Mass: 28302.760 Da / Num. of mol.: 4 / Mutation: S130A
Source method: isolated from a genetically manipulated source
Details: GB:PZN61876.1 / Source: (gene. exp.) Thermobifida fusca (bacteria) / Gene: cut-2.KW3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: cutinase

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Non-polymers , 6 types, 883 molecules

#2: Chemical ChemComp-C9C / 4-(2-hydroxyethyloxycarbonyl)benzoic acid / monohydroxyethyl terephthalate


Mass: 210.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 867 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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 Matthews: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 4
Details: 4% v/v PEG200; 0.8 M lithium sulfate; 0.1 M sodium acetate pH4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Apr 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.31→45.74 Å / Num. obs: 100354 / % possible obs: 99.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.0692 / Net I/σ(I): 14.96
Reflection shellResolution: 2.31→2.35 Å / Redundancy: 3.01 % / Rmerge(I) obs: 0.1601 / Mean I/σ(I) obs: 4.66 / Num. unique obs: 2675 / % possible all: 99.4

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Processing

Software
NameVersionClassification
SADABSdata scaling
PHENIX1.17.1refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5zoa

5zoa


Resolution: 2.31→42 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 3764 3.75 %
Rwork0.1661 96590 -
obs0.168 100354 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.19 Å2 / Biso mean: 17.3015 Å2 / Biso min: 4.95 Å2
Refinement stepCycle: final / Resolution: 2.31→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7976 0 110 867 8953
Biso mean--28.66 23.25 -
Num. residues----1044
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.31-2.340.25141410.1853472361394
2.34-2.370.22281340.170135993733100
2.37-2.40.24741460.180836283774100
2.4-2.440.28091400.173135533693100
2.44-2.470.24271480.183936913839100
2.47-2.510.25391350.18553546368199
2.51-2.550.23411460.17443652379899
2.55-2.60.23961410.19143484362598
2.6-2.640.2921230.19753349347293
2.64-2.70.27191460.200536703816100
2.7-2.750.29051440.183336153759100
2.75-2.810.22541420.184835783720100
2.81-2.880.29351410.181636223763100
2.88-2.950.26371370.18293659379699
2.95-3.030.2711380.18983527366599
3.03-3.120.21121250.19043518364397
3.12-3.220.25091470.18253583373099
3.22-3.330.24251380.16873557369598
3.33-3.460.23671410.16343612375399
3.47-3.620.22271350.16193585372099
3.62-3.810.17941430.14533612375599
3.81-4.050.16941440.13133536368099
4.05-4.360.14041330.12893603373699
4.36-4.80.16511270.12073636376399
4.8-5.50.14871520.1513557370999
5.5-6.920.21571380.18333594373299
6.92-420.20311390.16323552369198

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