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- PDB-8ais: Crystal structure of cutinase PsCut from Pseudomonas saudimassiliensis -

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Basic information

Entry
Database: PDB / ID: 8ais
TitleCrystal structure of cutinase PsCut from Pseudomonas saudimassiliensis
ComponentsLipase 1
KeywordsHYDROLASE / cutinase / ester bond / cleavage / PET
Function / homologyDienelactone hydrolase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold / hydrolase activity / ACETATE ION / Lipase 1
Function and homology information
Biological speciesPseudomonas saudimassiliensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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 / Refinement description
Category: citation / citation_author ...citation / citation_author / struct_ncs_dom / struct_ncs_dom_lim
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _struct_ncs_dom.details / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.end_auth_asym_id
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 / struct_ncs_dom_lim
Item: _citation.country / _struct_ncs_dom_lim.beg_auth_comp_id ..._citation.country / _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: Lipase 1
B: Lipase 1
C: Lipase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7764
Polymers100,7173
Non-polymers591
Water12,322684
1
A: Lipase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6322
Polymers33,5721
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipase 1


Theoretical massNumber of molelcules
Total (without water)33,5721
Polymers33,5721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lipase 1


Theoretical massNumber of molelcules
Total (without water)33,5721
Polymers33,5721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.786, 56.813, 105.796
Angle α, β, γ (deg.)90.000, 121.627, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-633-

HOH

21C-635-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53B
63C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNLEULEUAA40 - 30340 - 303
211GLNGLNLEULEUAA40 - 30340 - 303
322GLNGLNLEULEUAA40 - 30340 - 303
422GLNGLNLEULEUAA40 - 30340 - 303
533ASNASNGLUGLUBB37 - 30437 - 304
633ASNASNGLUGLUCC37 - 30437 - 304

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

#1: Protein Lipase 1


Mass: 33572.457 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas saudimassiliensis (bacteria)
Gene: lip1, BN1049_02053 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A078MGG8
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 2.02 Å3/Da / Density % sol: 39.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate pH 4.6, 8% PEG 4000

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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: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.56→52.38 Å / Num. obs: 113320 / % possible obs: 98.9 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.04 / Net I/σ(I): 9
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5312 / CC1/2: 0.473 / Rpim(I) all: 0.449 / % possible all: 93.7

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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: 1.56→52.377 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.519 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.083 / ESU R Free: 0.082
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.203 5514 4.903 %
Rwork0.1779 106959 -
all0.179 --
obs-112473 98.292 %
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: 21.566 Å2
Baniso -1Baniso -2Baniso -3
1--0.408 Å20 Å20.103 Å2
2--0.568 Å2-0 Å2
3----0.163 Å2
Refinement stepCycle: LAST / Resolution: 1.56→52.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6104 0 4 684 6792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0116278
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165447
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.648548
X-RAY DIFFRACTIONr_angle_other_deg0.5281.54812721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8245802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.4581052
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61510930
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.88610285
X-RAY DIFFRACTIONr_chiral_restr0.0790.2912
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027396
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021308
X-RAY DIFFRACTIONr_nbd_refined0.2140.21225
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.25280
X-RAY DIFFRACTIONr_nbtor_refined0.180.23131
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23141
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2504
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.230.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3480.227
X-RAY DIFFRACTIONr_nbd_other0.2390.2153
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.269
X-RAY DIFFRACTIONr_mcbond_it1.2661.2293206
X-RAY DIFFRACTIONr_mcbond_other1.2631.2293206
X-RAY DIFFRACTIONr_mcangle_it2.0171.8334002
X-RAY DIFFRACTIONr_mcangle_other2.0171.8354003
X-RAY DIFFRACTIONr_scbond_it1.671.3793072
X-RAY DIFFRACTIONr_scbond_other1.6641.3773071
X-RAY DIFFRACTIONr_scangle_it2.5732.0074544
X-RAY DIFFRACTIONr_scangle_other2.5732.0084545
X-RAY DIFFRACTIONr_lrange_it5.94820.0847289
X-RAY DIFFRACTIONr_lrange_other5.84518.3467124
X-RAY DIFFRACTIONr_ncsr_local_group_10.0770.058778
X-RAY DIFFRACTIONr_ncsr_local_group_20.070.058833
X-RAY DIFFRACTIONr_ncsr_local_group_30.0670.058923
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.076860.0501
12AX-RAY DIFFRACTIONLocal ncs0.076860.0501
23AX-RAY DIFFRACTIONLocal ncs0.070490.0501
24AX-RAY DIFFRACTIONLocal ncs0.070490.0501
35AX-RAY DIFFRACTIONLocal ncs0.067320.0501
36AX-RAY DIFFRACTIONLocal ncs0.067320.0501
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
1.56-1.60.393660.39674720.39683990.8860.87793.32060.395
1.6-1.6440.3613910.36573760.36581810.9020.89994.93950.361
1.644-1.6920.3823990.3472460.34279650.8940.91595.98240.334
1.692-1.7440.2943790.30871190.30877560.9330.93296.67350.296
1.744-1.8010.2873670.27570150.27575160.9470.9598.21710.259
1.801-1.8640.2633770.23768000.23872380.9550.96399.15720.22
1.864-1.9340.2363240.21666460.21770280.9640.9799.17470.195
1.934-2.0130.2143230.18464060.18667650.9720.97999.46780.166
2.013-2.1030.1973000.16762050.16865220.9760.98399.73930.152
2.103-2.2050.2023090.16158480.16361720.9740.98499.7570.149
2.205-2.3240.1893030.1555950.15259070.9790.98699.84760.14
2.324-2.4650.182550.1453330.14256000.980.98899.78570.133
2.465-2.6350.1622530.14550080.14652640.9840.98899.9430.139
2.635-2.8450.1712340.14246710.14449120.9820.98899.85750.139
2.845-3.1160.1632140.14242900.14345090.9840.98899.88910.142
3.116-3.4820.1661940.1539050.15141050.9860.98799.85380.155
3.482-4.0180.1551830.13634630.13736470.9860.9999.97260.146
4.018-4.9140.1391590.12329080.12430700.9910.99299.90230.14
4.914-6.9180.1731190.1523020.15124240.9860.98999.87620.166
6.918-52.3770.276650.1813310.18414010.9810.98499.64310.201
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)
11.3552-0.10810.07981.987-0.12561.62230.01810.0779-0.0014-0.13560.04730.0369-0.0104-0.0138-0.06530.0298-0.0207-0.00310.02260.00270.0039-12.7682-25.2766107.6025
21.71360.33150.21861.85130.17621.7193-0.05910.2509-0.05220.02640.0946-0.0197-0.00960.3377-0.03550.0051-0.01570.00750.1702-0.03080.016820.7889-25.9109136.4125
31.7279-0.2079-0.4061.89980.33061.8321-0.0029-0.0955-0.0493-0.03520.0548-0.0442-0.01980.0473-0.0520.0208-0.00750.01620.05010.01110.020817.4289-52.9559103.9966
Refinement TLS groupSelection: ALL

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