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- PDB-7qjs: Crystal structure of a cutinase enzyme from Thermobifida fusca YX... -

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Basic information

Entry
Database: PDB / ID: 7qjs
TitleCrystal structure of a cutinase enzyme from Thermobifida fusca YX (705)
ComponentsCutinase 2
KeywordsHYDROLASE / plastic degradation
Function / homology
Function and homology information


poly(ethylene terephthalate) hydrolase / cutinase activity / cutinase / periplasmic space / extracellular region
Similarity search - Function
Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Cutinase 2
Similarity search - Component
Biological speciesThermobifida fusca YX (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.429 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cutinase 2
B: Cutinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7456
Polymers59,2602
Non-polymers4854
Water6,702372
1
A: Cutinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9163
Polymers29,6301
Non-polymers2862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cutinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8283
Polymers29,6301
Non-polymers1982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.164, 150.212, 43.396
Angle α, β, γ (deg.)90.000, 92.509, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 1 - 263 / Label seq-ID: 2 - 264

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Cutinase 2 /


Mass: 29630.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca YX (bacteria) / Gene: cut2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9LVH9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene 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-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Cesium Chloride, 0.1 M MES pH 6.5, 30% (v/v) Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9119 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 1.429→75.106 Å / Num. obs: 57020 / % possible obs: 89 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.049 / Net I/σ(I): 9.3
Reflection shellResolution: 1.429→1.582 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2851 / CC1/2: 0.567 / Rpim(I) all: 0.493 / % possible all: 55.7

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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: 1.429→75.106 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.503 / SU ML: 0.066 / Cross valid method: FREE R-VALUE / ESU R: 0.104 / ESU R Free: 0.102
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2158 2826 4.953 %
Rwork0.1817 54231 -
all0.183 --
obs-57020 64.38 %
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: 16.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.008 Å20 Å20.019 Å2
2---0.281 Å2-0 Å2
3---0.271 Å2
Refinement stepCycle: LAST / Resolution: 1.429→75.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3982 0 29 372 4383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0134125
X-RAY DIFFRACTIONr_bond_other_d0.0010.0143820
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.6515619
X-RAY DIFFRACTIONr_angle_other_deg1.5391.5758790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3195522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.25320.455220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16915616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6721538
X-RAY DIFFRACTIONr_chiral_restr0.0960.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02988
X-RAY DIFFRACTIONr_nbd_refined0.2280.2893
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.23965
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22095
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.22091
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2334
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1910.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2190.219
X-RAY DIFFRACTIONr_nbd_other0.210.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2590.226
X-RAY DIFFRACTIONr_mcbond_it1.1731.3952076
X-RAY DIFFRACTIONr_mcbond_other1.1661.3932075
X-RAY DIFFRACTIONr_mcangle_it1.8272.082590
X-RAY DIFFRACTIONr_mcangle_other1.8282.0812591
X-RAY DIFFRACTIONr_scbond_it1.5511.592049
X-RAY DIFFRACTIONr_scbond_other1.5511.5912050
X-RAY DIFFRACTIONr_scangle_it2.4172.3033025
X-RAY DIFFRACTIONr_scangle_other2.4172.3053026
X-RAY DIFFRACTIONr_lrange_it4.32317.4434812
X-RAY DIFFRACTIONr_lrange_other4.18417.1244741
X-RAY DIFFRACTIONr_ncsr_local_group_10.070.058994
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.070050.05009
12BX-RAY DIFFRACTIONLocal ncs0.070050.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.429-1.4470.3770.275113X-RAY DIFFRACTION1.8121
1.447-1.4860.307230.261359X-RAY DIFFRACTION6.0799
1.486-1.5290.281520.261782X-RAY DIFFRACTION13.4516
1.529-1.5760.294660.2661304X-RAY DIFFRACTION22.6185
1.576-1.6280.3081010.2562110X-RAY DIFFRACTION38.0551
1.628-1.6850.2471410.242755X-RAY DIFFRACTION51.2476
1.685-1.7490.2452050.2363634X-RAY DIFFRACTION70.247
1.749-1.820.2582520.2324491X-RAY DIFFRACTION90.3601
1.82-1.9010.242660.2094637X-RAY DIFFRACTION97.3011
1.901-1.9940.2122160.1814483X-RAY DIFFRACTION97.794
1.994-2.1010.1932070.174252X-RAY DIFFRACTION98.0862
2.101-2.2290.1852020.1664085X-RAY DIFFRACTION98.3482
2.229-2.3830.2091890.163815X-RAY DIFFRACTION98.4752
2.383-2.5730.191880.1653574X-RAY DIFFRACTION98.9479
2.573-2.8190.2161410.1633296X-RAY DIFFRACTION99.0205
2.819-3.1510.1961840.172941X-RAY DIFFRACTION99.0177
3.151-3.6370.2031340.1732672X-RAY DIFFRACTION99.5742
3.637-4.4520.2231200.1562218X-RAY DIFFRACTION99.4894
4.452-6.2850.234800.1971742X-RAY DIFFRACTION99.6173
6.285-75.1060.211520.205967X-RAY DIFFRACTION99.5117
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.16480.0678-0.00110.2360.08220.2861-0.0069-0.0138-0.0178-0.00630.0019-0.01980.0083-0.01460.0050.0027-0.0030.00180.0065-0.00030.003115.13458.505420.6596
20.09780.1546-0.03850.4112-0.16430.38580.0072-0.01080.00510.00690.00590.0328-0.03230.0222-0.01310.004-0.0047-0.00070.00770.00330.00420.569742.6545-0.8351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 263
2X-RAY DIFFRACTION1ALLA301
3X-RAY DIFFRACTION2ALLB1 - 263
4X-RAY DIFFRACTION2ALLB302

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