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- PDB-7w1n: Complex structure of a leaf-branch compost cutinase variant LCC I... -

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Basic information

Entry
Database: PDB / ID: 7w1n
TitleComplex structure of a leaf-branch compost cutinase variant LCC ICCG_KRP
ComponentsLeaf-branch compost cutinase
KeywordsHYDROLASE / plastic degradation / mutant / catalysis
Function / homologyAlpha/beta hydrolase fold-5 / Alpha/beta hydrolase family / poly(ethylene terephthalate) hydrolase / acetylesterase activity / cutinase activity / cutinase / Alpha/Beta hydrolase fold / extracellular region / Leaf-branch compost cutinase
Function and homology information
Biological speciesUnknown prokaryotic organism (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.88 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 19, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leaf-branch compost cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8173
Polymers28,5921
Non-polymers2252
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-3 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.307, 60.442, 81.947
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 28592.045 Da / Num. of mol.: 1 / Mutation: A59K,V75R,Y127G, D238C, F243I,N248P, S283C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Unknown prokaryotic organism (environmental samples)
Plasmid: pET32Xa/LIC / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G9BY57, cutinase, poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
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: 2.01 Å3/Da / Density % sol: 38.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.3 / Details: 25% PEG Smear Medium, o.1 M Bicine pH 9.3

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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: Nov 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.88→33.94 Å / Num. obs: 18984 / % possible obs: 97.4 % / Redundancy: 5.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.046 / Rrim(I) all: 0.106 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.88-1.914.20.3549810.9040.1920.40680
8.97-24.824.40.032130.9990.0150.03396.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0refinement
Aimless0.6.3data scaling
PDB_EXTRACT3.27data extraction
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DS7

7ds7


Resolution: 1.88→33.94 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.665 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1652 934 4.9 %RANDOM
Rwork0.1372 ---
obs0.1387 17988 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 43.4 Å2 / Biso mean: 9.159 Å2 / Biso min: 2.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2---0.21 Å20 Å2
3----0.53 Å2
Refinement stepCycle: final / Resolution: 1.88→33.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 15 330 2301
Biso mean--23.81 21.7 -
Num. residues----258
LS refinement shellResolution: 1.88→1.929 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 70 -
Rwork0.198 1204 -
all-1274 -
obs--91 %

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