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- PDB-8ait: Crystal structure of cutinase PbauzCut from Pseudomonas bauzanensis -

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Basic information

Entry
Database: PDB / ID: 8ait
TitleCrystal structure of cutinase PbauzCut from Pseudomonas bauzanensis
ComponentsCutinase
KeywordsHYDROLASE / cutinase / ester bond / cleavage / PET
Function / homologyDienelactone hydrolase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold / hydrolase activity / Cutinase
Function and homology information
Biological speciesHalopseudomonas bauzanensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsZahn, M. / Allen, M.D. / Pickford, A.R. / McGeehan, J.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)Research England E3 United Kingdom
CitationJournal: ChemSusChem / Year: 2023
Title: Concentration-Dependent Inhibition of Mesophilic PETases on Poly(ethylene terephthalate) Can Be Eliminated by Enzyme Engineering.
Authors: Avilan, L. / Lichtenstein, B.R. / Konig, G. / Zahn, M. / Allen, M.D. / Oliveira, L. / Clark, M. / Bemmer, V. / Graham, R. / Austin, H.P. / Dominick, G. / Johnson, C.W. / Beckham, G.T. / ...Authors: Avilan, L. / Lichtenstein, B.R. / Konig, G. / Zahn, M. / Allen, M.D. / Oliveira, L. / Clark, M. / Bemmer, V. / Graham, R. / Austin, H.P. / Dominick, G. / Johnson, C.W. / Beckham, G.T. / McGeehan, J.E. / Pickford, A.R.
History
DepositionJul 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 22, 2023Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.3May 3, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8755
Polymers33,4901
Non-polymers3844
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.100, 52.900, 56.748
Angle α, β, γ (deg.)90.000, 106.305, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cutinase / Predicted dienelactone hydrolase


Mass: 33490.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halopseudomonas bauzanensis (bacteria) / Gene: SAMN04487855_0215, SAMN05216589_1412 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A031MKR8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.85 Å3/Da / Density % sol: 33.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium acetate 4.5, 50 % w/v PEG 400, 0.2 M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.24→52.9 Å / Num. obs: 69263 / % possible obs: 99.6 % / Redundancy: 3.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.063 / Net I/σ(I): 6.1
Reflection shellResolution: 1.24→1.26 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2 / Num. unique obs: 3366 / CC1/2: 0.563 / Rpim(I) all: 0.314 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CG1

4cg1


Resolution: 1.24→41.367 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / SU B: 2.396 / SU ML: 0.052 / Cross valid method: FREE R-VALUE / ESU R: 0.055 / ESU R Free: 0.056
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2379 3323 4.857 %
Rwork0.2142 65091 -
all0.215 --
obs-68414 98.534 %
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: 8.832 Å2
Baniso -1Baniso -2Baniso -3
1--0.221 Å2-0 Å20.147 Å2
2---0.442 Å2-0 Å2
3---0.493 Å2
Refinement stepCycle: LAST / Resolution: 1.24→41.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1995 0 20 265 2280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122070
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161778
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.642826
X-RAY DIFFRACTIONr_angle_other_deg0.5951.5464151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1065263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.0961017
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61810299
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.6781093
X-RAY DIFFRACTIONr_chiral_restr0.090.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022420
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02428
X-RAY DIFFRACTIONr_nbd_refined0.230.2399
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21720
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21033
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21020
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.250.2195
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1110.215
X-RAY DIFFRACTIONr_nbd_other0.1810.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2190.222
X-RAY DIFFRACTIONr_mcbond_it0.4380.4051049
X-RAY DIFFRACTIONr_mcbond_other0.4240.4051049
X-RAY DIFFRACTIONr_mcangle_it0.7080.6071310
X-RAY DIFFRACTIONr_mcangle_other0.7090.6071311
X-RAY DIFFRACTIONr_scbond_it0.8670.5151021
X-RAY DIFFRACTIONr_scbond_other0.7860.4951005
X-RAY DIFFRACTIONr_scangle_it1.2450.7461515
X-RAY DIFFRACTIONr_scangle_other1.210.7131492
X-RAY DIFFRACTIONr_lrange_it4.4949.9082420
X-RAY DIFFRACTIONr_lrange_other4.1716.9992330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.24-1.2720.3722110.33147540.33351180.9120.91397.01060.32
1.272-1.3070.342260.32446140.32549600.9220.91897.58070.312
1.307-1.3450.3222200.31144960.31148580.910.92397.0770.296
1.345-1.3860.3242360.343700.30147330.9240.93197.31670.287
1.386-1.4320.3012250.28141850.28245220.9370.94297.52320.265
1.432-1.4820.2762120.27341520.27344280.9440.9498.55460.257
1.482-1.5380.2531960.23640000.23742530.9560.95798.65980.222
1.538-1.60.2532100.23338550.23441060.9490.95899.00150.221
1.6-1.6710.2591850.2136940.21239240.9540.96798.85320.201
1.671-1.7530.2321850.20135590.20337710.9550.96999.2840.195
1.753-1.8470.2351580.19134060.19235910.9580.97299.24810.186
1.847-1.9590.1841660.18432260.18434070.9760.97499.55970.184
1.959-2.0940.2231540.18929960.19131680.9570.97199.43180.193
2.094-2.2620.2111550.17827930.1829690.970.97599.29270.184
2.262-2.4770.2161450.18525810.18627380.9510.97299.56170.192
2.477-2.7680.2261010.18223930.18425020.9530.97599.68030.195
2.768-3.1940.1991020.18620620.18721770.970.97499.40280.201
3.194-3.9050.1981080.17617760.17718880.9640.97799.78810.193
3.905-5.4990.195740.18113800.18214580.970.97799.72570.213
5.499-41.3670.245540.2137870.2158410.9690.9711000.247
Refinement TLS params.Method: refined / Origin x: -5.1423 Å / Origin y: 1.408 Å / Origin z: 14.3448 Å
111213212223313233
T0.0034 Å20.0006 Å2-0.0017 Å2-0.0561 Å20.0048 Å2--0.0025 Å2
L0.6608 °20.1067 °2-0.0305 °2-0.9413 °20.1076 °2--0.6226 °2
S-0.0083 Å °0.0342 Å °0.0036 Å °-0.048 Å °0.0059 Å °0.0079 Å °-0.003 Å °0.0215 Å °0.0023 Å °
Refinement TLS groupSelection: ALL

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