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- PDB-7ds7: The Crystal Structure of Leaf-branch compost cutinase from Biortus. -

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Basic information

Entry
Database: PDB / ID: 7ds7
TitleThe Crystal Structure of Leaf-branch compost cutinase from Biortus.
ComponentsLeaf-branch compost cutinase
KeywordsHYDROLASE / catalytic activity / hydrolase activity / acting on ester bonds
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
CITRIC ACID / IMIDAZOLE / Leaf-branch compost cutinase
Similarity search - Component
Biological speciesUnknown prokaryotic organism (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWang, F. / Lv, Z. / Cheng, W. / Lin, D. / Chu, F. / Xu, X. / Tan, J.
CitationJournal: To Be Published
Title: The Crystal Structure of Leaf-branch compost cutinase from Biortus.
Authors: Wang, F. / Lv, Z. / Cheng, W. / Lin, D. / Chu, F. / Xu, X. / Tan, J.
History
DepositionDec 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary
Category: pdbx_contact_author / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_contact_author.email / _pdbx_entry_details.has_protein_modification

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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)30,1594
Polymers29,8051
Non-polymers3533
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint0 kcal/mol
Surface area9910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.412, 109.412, 35.137
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 29805.250 Da / Num. of mol.: 1 / Mutation: Y127G,S165A,D238C,F243I,S283C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Unknown prokaryotic organism (environmental samples)
Production host: Escherichia coli (E. coli)
References: UniProt: G9BY57, cutinase, poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.04 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.6M imidazole, 0.1M tri-sodium citrate PH7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.15→47.38 Å / Num. obs: 13146 / % possible obs: 98.1 % / Redundancy: 11 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 22.1
Reflection shellResolution: 2.15→2.22 Å / Rmerge(I) obs: 0.262 / Num. unique obs: 1117

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6tht

6tht


Resolution: 2.15→47.38 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.606 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.286 / ESU R Free: 0.206
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2273 678 5.158 %
Rwork0.1803 12466 -
all0.183 --
obs-13144 98.082 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 9.937 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.075 Å2-0 Å2
2---0.15 Å20 Å2
3---0.485 Å2
Refinement stepCycle: LAST / Resolution: 2.15→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 24 114 2086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132040
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171812
X-RAY DIFFRACTIONr_angle_refined_deg1.21.6452796
X-RAY DIFFRACTIONr_angle_other_deg1.1251.5644196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5085263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.64220.7100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.40315285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0291516
X-RAY DIFFRACTIONr_chiral_restr0.0430.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022358
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02450
X-RAY DIFFRACTIONr_nbd_refined0.1830.2380
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1670.21762
X-RAY DIFFRACTIONr_nbtor_refined0.150.2984
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.2831
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2135
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0840.29
X-RAY DIFFRACTIONr_nbd_other0.1840.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0980.213
X-RAY DIFFRACTIONr_mcbond_it0.2021.0521043
X-RAY DIFFRACTIONr_mcbond_other0.2011.0511042
X-RAY DIFFRACTIONr_mcangle_it0.3731.5751306
X-RAY DIFFRACTIONr_mcangle_other0.3731.5761307
X-RAY DIFFRACTIONr_scbond_it0.1611.105997
X-RAY DIFFRACTIONr_scbond_other0.1491.098994
X-RAY DIFFRACTIONr_scangle_it0.2931.6481489
X-RAY DIFFRACTIONr_scangle_other0.2931.6511490
X-RAY DIFFRACTIONr_lrange_it1.66412.6872257
X-RAY DIFFRACTIONr_lrange_other1.66412.7042258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.2060.249690.198885X-RAY DIFFRACTION94.5491
2.206-2.2670.222510.198885X-RAY DIFFRACTION99.6805
2.267-2.3320.302530.192826X-RAY DIFFRACTION93.9103
2.332-2.4040.288400.189849X-RAY DIFFRACTION98.9978
2.404-2.4830.281410.18795X-RAY DIFFRACTION96.5358
2.483-2.570.266380.204784X-RAY DIFFRACTION97.7408
2.57-2.6670.258380.19783X-RAY DIFFRACTION98.5594
2.667-2.7760.184360.184720X-RAY DIFFRACTION97.4227
2.776-2.8990.214340.189717X-RAY DIFFRACTION99.2074
2.899-3.040.246460.197664X-RAY DIFFRACTION97.931
3.04-3.2050.22340.195653X-RAY DIFFRACTION98.1429
3.205-3.3990.211270.187611X-RAY DIFFRACTION100
3.399-3.6330.2300.187586X-RAY DIFFRACTION98.7179
3.633-3.9240.194210.167559X-RAY DIFFRACTION99.4854
3.924-4.2980.187330.145490X-RAY DIFFRACTION100
4.298-4.8040.17230.146465X-RAY DIFFRACTION99.389
4.804-5.5440.184250.158394X-RAY DIFFRACTION99.7619
5.544-6.7850.162100.162366X-RAY DIFFRACTION99.7347
6.785-9.570.218190.125271X-RAY DIFFRACTION100
9.57-47.380.414100.173163X-RAY DIFFRACTION98.8571

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