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- PDB-7w44: Complex structure of a leaf-branch compost cutinase variant LCC I... -

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Basic information

Entry
Database: PDB / ID: 7w44
TitleComplex structure of a leaf-branch compost cutinase variant LCC ICCG_RIP
ComponentsLeaf-branch compost cutinase
KeywordsHYDROLASE / plastic degradation / mutant / catalysis
Function / homology
Function and homology information


acetylesterase activity / poly(ethylene terephthalate) hydrolase / cutinase / cutinase activity / extracellular region
Similarity search - Function
Cutinase / PET hydrolase-like / : / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
IMIDAZOLE / Leaf-branch compost cutinase
Similarity search - Component
Biological speciesunidentified prokaryotic organism (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 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 26, 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 1.2Nov 20, 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)57,2315
Polymers57,0382
Non-polymers1933
Water11,079615
1
A: Leaf-branch compost cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5812
Polymers28,5191
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leaf-branch compost cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6503
Polymers28,5191
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.567, 153.270, 118.236
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-625-

HOH

21B-633-

HOH

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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: 28518.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified prokaryotic organism (environmental samples)
Plasmid: pET46Ek /LIC / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G9BY57, cutinase, poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 615 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 12% w/v PEG 20,000

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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: Oct 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.85→24.94 Å / Num. obs: 49376 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.038 / Rrim(I) all: 0.105 / Net I/σ(I): 12.7 / Num. measured all: 336582 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.894.70.461428530400.9240.2170.5113.2100
9.06-24.9470.04231184480.9980.0170.04627.594.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.6.3data scaling
PDB_EXTRACT3.27data extraction
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DS7

7ds7


Resolution: 1.85→24.94 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.519 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 2483 5 %RANDOM
Rwork0.1508 ---
obs0.1526 47432 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.59 Å2 / Biso mean: 15.706 Å2 / Biso min: 1.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20 Å2
2---1.06 Å20 Å2
3---0.17 Å2
Refinement stepCycle: final / Resolution: 1.85→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3890 0 13 615 4518
Biso mean--30.13 29.35 -
Num. residues----514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134025
X-RAY DIFFRACTIONr_bond_other_d0.0010.0143705
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.6475512
X-RAY DIFFRACTIONr_angle_other_deg1.4951.578499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0115520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.60820.348201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.60715572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4851534
X-RAY DIFFRACTIONr_chiral_restr0.0830.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024667
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02989
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 174 -
Rwork0.221 3417 -
all-3591 -
obs--97.74 %

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