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- PDB-7vvc: Crystal structure of inactive mutant of leaf-branch compost cutin... -

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Basic information

Entry
Database: PDB / ID: 7vvc
TitleCrystal structure of inactive mutant of leaf-branch compost cutinase variant
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
ACETATE ION / ACETIC ACID / Leaf-branch compost cutinase
Similarity search - Component
Biological speciesUnknown prokaryotic organism (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 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 1.2Nov 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)57,3979
Polymers56,9542
Non-polymers4437
Water12,917717
1
A: Leaf-branch compost cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6694
Polymers28,4771
Non-polymers1923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-9 kcal/mol
Surface area9680 Å2
MethodPISA
2
B: Leaf-branch compost cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7285
Polymers28,4771
Non-polymers2514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-9 kcal/mol
Surface area10080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.429, 84.702, 147.390
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: 28476.861 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, 724 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 717 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.27 Å3/Da / Density % sol: 45.82 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Ammonium Acetate,Sodium Acetate trihydrate,Polyethylene Glycol 4000, Glycerol

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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: Jul 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.82→25 Å / Num. obs: 45015 / % possible obs: 99.8 % / Redundancy: 4.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.038 / Rrim(I) all: 0.085 / Net I/σ(I): 12.4
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.25 / Num. unique obs: 2722 / CC1/2: 0.952 / Rpim(I) all: 0.155 / Rrim(I) all: 0.295 / % possible all: 99.2

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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: 1.82→25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.718 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1977 2390 5.1 %RANDOM
Rwork0.1511 ---
obs0.1534 44723 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.52 Å2 / Biso mean: 14.49 Å2 / Biso min: 5.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.03 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.82→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3924 0 24 717 4665
Biso mean--29.46 28.88 -
Num. residues----521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134140
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173691
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.6455679
X-RAY DIFFRACTIONr_angle_other_deg1.5071.5648545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9835541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.70120.583206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.47215583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5111534
X-RAY DIFFRACTIONr_chiral_restr0.0840.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024813
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02917
LS refinement shellResolution: 1.82→1.867 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 161 -
Rwork0.202 3125 -
all-3286 -
obs--96.08 %

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