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- PDB-8jmp: Structure of a leaf-branch compost cutinase, ICCG in complex with... -

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Basic information

Entry
Database: PDB / ID: 8jmp
TitleStructure of a leaf-branch compost cutinase, ICCG in complex with 1,4-butanediol terephthalate
ComponentsLeaf-branch compost cutinase
KeywordsHYDROLASE / PETase / cutinase / enzyme engineering / PBAT degradation
Function / homology
Function and homology information


acetylesterase activity / poly(ethylene terephthalate) hydrolase / cutinase activity / cutinase / extracellular region
Similarity search - Function
Alpha/beta hydrolase fold-5 / Alpha/beta hydrolase family / : / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-EMX / Leaf-branch compost cutinase
Similarity search - Component
Biological speciesunidentified prokaryotic organism (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYang, Y. / Xue, T. / Zheng, Y. / Cheng, S. / Guo, R.-T. / Chen, C.-C.
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) China
CitationJournal: J Hazard Mater / Year: 2023
Title: Remodeling the polymer-binding cavity to improve the efficacy of PBAT-degrading enzyme.
Authors: Yang, Y. / Cheng, S. / Zheng, Y. / Xue, T. / Huang, J.W. / Zhang, L. / Yang, Y. / Guo, R.T. / Chen, C.C.
History
DepositionJun 5, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: Leaf-branch compost cutinase
B: Leaf-branch compost cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0994
Polymers55,6722
Non-polymers4262
Water12,016667
1
A: Leaf-branch compost cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2633
Polymers27,8361
Non-polymers4262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-9 kcal/mol
Surface area9880 Å2
MethodPISA
2
B: Leaf-branch compost cutinase


Theoretical massNumber of molelcules
Total (without water)27,8361
Polymers27,8361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.190, 84.928, 147.979
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Leaf-branch compost cutinase / LC-cutinase / LCC / PET-digesting enzyme / Poly(ethylene terephthalate) hydrolase / PET hydrolase / PETase


Mass: 27836.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified prokaryotic organism (environmental samples)
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G9BY57, cutinase, poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EMX / 4-[4-(4-carboxyphenyl)carbonyloxybutoxycarbonyl]benzoic acid / 4,4'-((Butane-1,4-diylbis(oxy))bis(carbonyl))dibenzoic acid


Mass: 386.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / Source method: isolated from a natural source / Formula: H2O
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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 298 K / Method: evaporation
Details: 20% v/v PEG 8000 and 0.1 M sodium cacodylate, pH 6.5

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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 II / Detector: PIXEL / Date: Apr 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.9→36.94 Å / Num. obs: 78612 / % possible obs: 99.4 % / Redundancy: 9.23 % / CC1/2: 1 / Rmerge(I) obs: 0.058 / Net I/σ(I): 25.33
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.1439 / Mean I/σ(I) obs: 6.26 / Num. unique obs: 1906 / CC1/2: 0.989

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
SAINTdata reduction
SADABSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→31.62 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 19.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1955 3772 4.8 %
Rwork0.1537 --
obs0.1558 78612 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→31.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3894 0 29 670 4593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064054
X-RAY DIFFRACTIONf_angle_d0.795555
X-RAY DIFFRACTIONf_dihedral_angle_d17.769587
X-RAY DIFFRACTIONf_chiral_restr0.051625
X-RAY DIFFRACTIONf_plane_restr0.006732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.21711420.17252814X-RAY DIFFRACTION100
1.92-1.950.23621420.18852790X-RAY DIFFRACTION100
1.95-1.980.3271410.18812789X-RAY DIFFRACTION100
1.98-20.29011390.18332753X-RAY DIFFRACTION100
2-2.030.23461370.16792790X-RAY DIFFRACTION100
2.03-2.070.24611470.16112831X-RAY DIFFRACTION100
2.07-2.10.21861350.1682749X-RAY DIFFRACTION100
2.1-2.140.20861370.16722794X-RAY DIFFRACTION100
2.14-2.170.23511400.16432806X-RAY DIFFRACTION100
2.18-2.220.21771420.15912757X-RAY DIFFRACTION100
2.22-2.260.20441430.15492797X-RAY DIFFRACTION100
2.26-2.310.19711370.14642799X-RAY DIFFRACTION100
2.31-2.360.18571410.15272771X-RAY DIFFRACTION100
2.36-2.420.18761460.16052844X-RAY DIFFRACTION100
2.42-2.490.24311330.15822708X-RAY DIFFRACTION100
2.49-2.560.2031390.16142823X-RAY DIFFRACTION100
2.56-2.650.21911400.16732756X-RAY DIFFRACTION100
2.65-2.740.18221450.15962815X-RAY DIFFRACTION100
2.74-2.850.19691380.15282768X-RAY DIFFRACTION100
2.85-2.980.19281360.1552781X-RAY DIFFRACTION100
2.98-3.140.19911430.15352818X-RAY DIFFRACTION100
3.14-3.330.22591390.14592741X-RAY DIFFRACTION100
3.33-3.590.16731400.14782800X-RAY DIFFRACTION100
3.59-3.950.17311430.13352757X-RAY DIFFRACTION99
3.95-4.520.13191410.12012728X-RAY DIFFRACTION98
4.52-5.690.15011340.13522708X-RAY DIFFRACTION98
5.69-31.620.1611320.17242553X-RAY DIFFRACTION92

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