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- PDB-7xtu: The structure of TfCut S130A -

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Basic information

Entry
Database: PDB / ID: 7xtu
TitleThe structure of TfCut S130A
Componentsalpha/beta hydrolase
KeywordsHYDROLASE / PET hydrolase / PBAT hydrolase / enzyme engineering / cutinase
Function / homologyACETATE ION / : / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 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

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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)114,67724
Polymers113,2114
Non-polymers1,46620
Water14,718817
1
A: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8338
Polymers28,3031
Non-polymers5307
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6897
Polymers28,3031
Non-polymers3866
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5744
Polymers28,3031
Non-polymers2713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5815
Polymers28,3031
Non-polymers2784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.414, 91.414, 247.696
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-503-

HOH

21C-671-

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, 837 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 817 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.64 Å3/Da / Density % sol: 53.39 %
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 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.43→39.99 Å / Num. obs: 86890 / % possible obs: 99.9 % / Redundancy: 9.42 % / Rmerge(I) obs: 0.0949 / Net I/σ(I): 10.24
Reflection shellResolution: 2.43→2.47 Å / Redundancy: 4.47 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 2221 / % possible all: 99.8

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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: 2.43→39.58 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2255 3757 4.32 %
Rwork0.1752 83133 -
obs0.1773 86890 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.5 Å2 / Biso mean: 19.2878 Å2 / Biso min: 1.09 Å2
Refinement stepCycle: final / Resolution: 2.43→39.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7976 0 96 817 8889
Biso mean--28.75 25.17 -
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 (%)
2.43-2.460.29951240.24833009313396
2.46-2.490.2861430.23633053319699
2.49-2.530.25951430.219530903233100
2.53-2.560.23381400.223083322399
2.56-2.60.30211440.21443079322399
2.6-2.640.30481390.22782977311699
2.64-2.690.26431460.216630913237100
2.69-2.730.29991300.213430853215100
2.73-2.780.30751460.217231293275100
2.78-2.830.29191420.205530443186100
2.84-2.890.24681330.192630833216100
2.89-2.960.18591540.192231133267100
2.96-3.020.21921440.177230783222100
3.02-3.10.20271360.183830623198100
3.1-3.180.28221370.185530863223100
3.18-3.280.23151380.178730983236100
3.28-3.380.23731400.169931403280100
3.38-3.50.24591460.175530763222100
3.5-3.640.25171360.168530683204100
3.64-3.810.18381400.142931063246100
3.81-4.010.15521380.128130603198100
4.01-4.260.16861320.124430943226100
4.26-4.590.17951320.123831013233100
4.59-5.050.16241480.133830963244100
5.05-5.780.23521280.179231003228100
5.78-7.270.23231420.188830623204100
7.28-39.580.18131360.17533070320699

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