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- PDB-7qjt: Crystal structure of a cutinase enzyme from Thermobifida cellulos... -

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Basic information

Entry
Database: PDB / ID: 7qjt
TitleCrystal structure of a cutinase enzyme from Thermobifida cellulosilytica TB100 (711)
Componentscutinase (711)
KeywordsHYDROLASE / plastic degradation
Biological speciesThermobifida cellulosilytica TB100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsZahn, M. / Shakespeare, T.J. / Beckham, G.T. / McGeehan, J.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)Research England E3 funding United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Sourcing thermotolerant poly(ethylene terephthalate) hydrolase scaffolds from natural diversity
Authors: Erickson, E. / Gado, J.E. / Avilan, L. / Bratti, F. / Brizendine, R.K. / Cox, P.A. / Gill, R. / Graham, R. / Kim, D.J. / Konig, G. / Michener, W.E. / Poudel, S. / Ramirez, K.J. / ...Authors: Erickson, E. / Gado, J.E. / Avilan, L. / Bratti, F. / Brizendine, R.K. / Cox, P.A. / Gill, R. / Graham, R. / Kim, D.J. / Konig, G. / Michener, W.E. / Poudel, S. / Ramirez, K.J. / Shakespeare, T.J. / Zahn, M. / Boyd, E.S. / Payne, C.M. / DuBois, J.L. / Pickford, A.R. / Beckham, G.T. / McGeehan, J.E.
History
DepositionDec 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

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Assembly

Deposited unit
A: cutinase (711)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5066
Polymers29,1461
Non-polymers3595
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-17 kcal/mol
Surface area10720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.297, 109.297, 44.184
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-593-

HOH

21A-609-

HOH

31A-632-

HOH

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Components

#1: Protein cutinase (711)


Mass: 29146.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida cellulosilytica TB100 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium Chloride Hexahydrate, 0.1 M Tris pH 8.5, 20 % (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.777→77.285 Å / Num. obs: 17061 / % possible obs: 87.1 % / Redundancy: 26.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.639 / Rpim(I) all: 0.126 / Net I/σ(I): 6.3
Reflection shellResolution: 1.777→1.965 Å / Redundancy: 22 % / Rmerge(I) obs: 3.127 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 855 / CC1/2: 0.615 / Rpim(I) all: 0.65 / % possible all: 64.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5zoa

5zoa


Resolution: 1.78→77.285 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.904 / SU B: 8.471 / SU ML: 0.132 / Cross valid method: FREE R-VALUE / ESU R: 0.218 / ESU R Free: 0.19
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2415 853 5.001 %
Rwork0.1817 16204 -
all0.185 --
obs-17057 64.969 %
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: 18.271 Å2
Baniso -1Baniso -2Baniso -3
1-0.359 Å2-0 Å2-0 Å2
2--0.359 Å2-0 Å2
3----0.717 Å2
Refinement stepCycle: LAST / Resolution: 1.78→77.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 19 241 2304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132115
X-RAY DIFFRACTIONr_bond_other_d0.0010.0141912
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.6512884
X-RAY DIFFRACTIONr_angle_other_deg1.431.574408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9065266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.15820.625112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38515305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7441518
X-RAY DIFFRACTIONr_chiral_restr0.0810.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022418
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02494
X-RAY DIFFRACTIONr_nbd_refined0.2270.2462
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.21888
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21017
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2978
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2199
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0520.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1360.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2880.226
X-RAY DIFFRACTIONr_nbd_other0.2570.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1730.217
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0820.22
X-RAY DIFFRACTIONr_mcbond_it1.2761.5891067
X-RAY DIFFRACTIONr_mcbond_other1.2681.5881066
X-RAY DIFFRACTIONr_mcangle_it2.2182.3781332
X-RAY DIFFRACTIONr_mcangle_other2.2182.381333
X-RAY DIFFRACTIONr_scbond_it1.4941.7911047
X-RAY DIFFRACTIONr_scbond_other1.4941.7931048
X-RAY DIFFRACTIONr_scangle_it2.5382.6151552
X-RAY DIFFRACTIONr_scangle_other2.5372.6161553
X-RAY DIFFRACTIONr_lrange_it5.29220.0322450
X-RAY DIFFRACTIONr_lrange_other4.93919.2692380
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
1.78-1.8260.46510.254920.256191500.84.85640.237
1.826-1.8760.20760.2721670.2718310.7530.7779.44840.26
1.876-1.9310.374200.272740.27818200.7850.79416.15380.249
1.931-1.990.256330.2535200.25317570.8370.83231.47410.239
1.99-2.0550.322400.2787090.2816860.8270.83244.42470.261
2.055-2.1270.291500.2628630.26416640.8520.8454.86780.231
2.127-2.2070.321530.2349740.23815950.80.86664.38870.213
2.207-2.2980.274500.21910740.22115390.8140.87273.03440.193
2.298-2.40.276700.20611850.2114720.870.88785.25810.178
2.4-2.5170.237650.20512760.20714200.8990.90394.43660.174
2.517-2.6530.261640.1912810.19313600.8950.92198.89710.157
2.653-2.8130.221630.17112320.17412960.9150.94499.92280.144
2.813-3.0070.251610.16111450.16612060.9380.9511000.134
3.007-3.2480.166460.14410810.14511270.9520.9591000.121
3.248-3.5570.214640.1479950.15110590.9350.9591000.127
3.557-3.9760.203400.1529170.1549570.9470.9631000.136
3.976-4.5890.22430.1458120.1488550.9470.9711000.138
4.589-5.6150.224410.1727030.1757440.9440.961000.16
5.615-7.9210.269260.1945580.1975840.9490.9491000.18
7.921-77.2850.225170.1723460.1743630.960.9761000.176
Refinement TLS params.Method: refined / Origin x: -2.8901 Å / Origin y: 26.549 Å / Origin z: -5.7805 Å
111213212223313233
T0.0011 Å2-0.0009 Å2-0.0021 Å2-0.0023 Å20.0023 Å2--0.0269 Å2
L0.2824 °2-0.0059 °2-0.0888 °2-0.3098 °2-0.0747 °2--0.2621 °2
S-0.0014 Å °-0.006 Å °-0.0152 Å °0.0055 Å °0.0078 Å °0.0007 Å °-0.005 Å °-0.008 Å °-0.0064 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 267
2X-RAY DIFFRACTION1ALLA301

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