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- PDB-7vve: Complex structure of a leaf-branch compost cutinase variant in co... -

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Basic information

Entry
Database: PDB / ID: 7vve
TitleComplex structure of a leaf-branch compost cutinase variant in complex with mono(2-hydroxyethyl) terephthalic acid
ComponentsLeaf-branch compost cutinase
KeywordsHYDROLASE / plastic degradation / activity
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
4-(2-hydroxyethyloxycarbonyl)benzoic acid / DI(HYDROXYETHYL)ETHER / Leaf-branch compost cutinase
Similarity search - Component
Biological speciesUnknown prokaryotic organism (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsNiu, D. / Zeng, W. / Huang, J.W. / Chen, C.C. / Liu, W.D. / Guo, R.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2022
Title: Substrate-Binding Mode of a Thermophilic PET Hydrolase and Engineering the Enzyme to Enhance the Hydrolytic Efficacy.
Authors: Zeng, W. / Li, X. / Yang, Y. / Min, J. / Huang, J.-W. / Liu, W. / Niu, D. / Yang, X. / Han, X. / Zhang, L. / Dai, L. / Chen, C.-C. / Guo, R.-T.
History
DepositionNov 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 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)56,61110
Polymers55,6722
Non-polymers9398
Water12,070670
1
A: Leaf-branch compost cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5257
Polymers27,8361
Non-polymers6896
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-9 kcal/mol
Surface area9730 Å2
MethodPISA
2
B: Leaf-branch compost cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0863
Polymers27,8361
Non-polymers2502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-9 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.277, 85.090, 147.746
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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.) Unknown prokaryotic organism (environmental samples)
Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G9BY57, cutinase, poly(ethylene terephthalate) hydrolase

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Non-polymers , 5 types, 678 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Calcium chloride 0.1 M Sodium Cacodylate pH 6.5 16-20% w/v PEG 8000

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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: Dec 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.98→25 Å / Num. obs: 37584 / % possible obs: 96.7 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.016 / Rrim(I) all: 0.041 / Net I/σ(I): 31.6
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.073 / Num. unique obs: 2206 / CC1/2: 0.995 / Rpim(I) all: 0.034 / Rrim(I) all: 0.08 / % possible all: 81.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.6.3data scaling
PDB_EXTRACT3.27data extraction
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DS7

7ds7


Resolution: 1.98→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.776 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1867 1835 5 %RANDOM
Rwork0.1385 ---
obs0.1409 35218 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.46 Å2 / Biso mean: 13.293 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.98→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3908 0 57 670 4635
Biso mean--33.9 26.79 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134101
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173665
X-RAY DIFFRACTIONr_angle_refined_deg1.721.6555603
X-RAY DIFFRACTIONr_angle_other_deg1.4821.5718477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1125522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.47320.64203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29515576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1531533
X-RAY DIFFRACTIONr_chiral_restr0.0860.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02901
LS refinement shellResolution: 1.98→2.021 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.231 120 -
Rwork0.152 2272 -
obs--84.79 %

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