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- PDB-7qjp: Crystal structure of a cutinase enzyme from Saccharopolyspora fla... -

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Basic information

Entry
Database: PDB / ID: 7qjp
TitleCrystal structure of a cutinase enzyme from Saccharopolyspora flava (611)
ComponentsCutinase
KeywordsHYDROLASE / plastic degradation
Function / homologyCutinase / PET hydrolase-like / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / Cutinase
Function and homology information
Biological speciesSaccharopolyspora flava (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.561 Å
AuthorsZahn, M. / Avilan, L. / 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 2.0Apr 24, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_rmsd_bond.auth_seq_id_1 / _pdbx_validate_rmsd_bond.auth_seq_id_2 / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id
Revision 2.1Oct 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3112
Polymers29,1171
Non-polymers1941
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint4 kcal/mol
Surface area9830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.336, 89.336, 74.324
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-649-

HOH

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Components

#1: Protein Cutinase


Mass: 29117.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora flava (bacteria) / Gene: SAMN05660874_00127 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1I6NU60
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.94 Å3/Da / Density % sol: 58.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20 % PEG 3350, 0.2 M sodium fluoride, 0.1 M Bis-Tris propane pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8153 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8153 Å / Relative weight: 1
ReflectionResolution: 1.561→77.367 Å / Num. obs: 40562 / % possible obs: 94.9 % / Redundancy: 17.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.034 / Net I/σ(I): 12.5
Reflection shellResolution: 1.561→1.652 Å / Rmerge(I) obs: 2.153 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2028 / CC1/2: 0.632 / Rpim(I) all: 0.548

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1jfr

1jfr


Resolution: 1.561→77.367 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.911 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.066 / ESU R Free: 0.068
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1653 1981 4.884 %
Rwork0.1406 38581 -
all0.142 --
obs-40562 82.749 %
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: 21.693 Å2
Baniso -1Baniso -2Baniso -3
1-0.013 Å20.007 Å20 Å2
2--0.013 Å2-0 Å2
3----0.043 Å2
Refinement stepCycle: LAST / Resolution: 1.561→77.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 13 314 2276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0132039
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171826
X-RAY DIFFRACTIONr_angle_refined_deg2.0131.6532795
X-RAY DIFFRACTIONr_angle_other_deg1.6171.5774253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8045266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09223.81497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.03615297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.956158
X-RAY DIFFRACTIONr_chiral_restr0.1080.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022344
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02432
X-RAY DIFFRACTIONr_nbd_refined0.2230.2391
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.21774
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21020
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2941
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.2233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.5550.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2530.22
X-RAY DIFFRACTIONr_nbd_other0.1780.223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2770.223
X-RAY DIFFRACTIONr_mcbond_it1.171.471037
X-RAY DIFFRACTIONr_mcbond_other1.1181.4681036
X-RAY DIFFRACTIONr_mcangle_it1.7612.21297
X-RAY DIFFRACTIONr_mcangle_other1.7682.2011298
X-RAY DIFFRACTIONr_scbond_it1.8861.6521002
X-RAY DIFFRACTIONr_scbond_other1.8851.6561003
X-RAY DIFFRACTIONr_scangle_it2.7382.4111493
X-RAY DIFFRACTIONr_scangle_other2.7372.4131494
X-RAY DIFFRACTIONr_lrange_it5.87719.9762333
X-RAY DIFFRACTIONr_lrange_other5.57618.4912238
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
1.561-1.6020.248340.2585090.25835690.8320.83115.21430.253
1.602-1.6450.271620.24511710.24634820.8560.85535.41070.235
1.645-1.6930.227940.22517190.22534150.870.87853.08930.211
1.693-1.7450.2311100.20820930.20932900.8990.89866.96050.189
1.745-1.8020.248870.20526600.20632070.8930.91385.65640.18
1.802-1.8660.1951580.18729610.18831510.9290.93398.98450.161
1.866-1.9360.191600.16828210.1729810.9480.9461000.142
1.936-2.0150.1711210.14927420.1528630.9560.9631000.126
2.015-2.1050.1661450.13926280.1427730.9630.9681000.118
2.105-2.2070.1691590.13324980.13526570.9660.9711000.114
2.207-2.3260.1521230.12324070.12525300.9710.9761000.107
2.326-2.4670.175890.12723160.12824050.9610.9741000.11
2.467-2.6380.1661130.12121460.12322590.9730.9761000.108
2.638-2.8490.171290.13419820.13621110.9670.9751000.124
2.849-3.120.168930.1318560.13219490.970.9781000.123
3.12-3.4880.17770.1416830.14217600.9690.9761000.136
3.488-4.0260.127880.11914910.1215790.9840.9841000.123
4.026-4.9270.107560.10612910.10613470.9880.9881000.116
4.927-6.9540.224470.15710120.1610590.9630.9731000.166
6.954-77.3670.152360.1715950.176310.9770.9681000.192
Refinement TLS params.Method: refined / Origin x: 21.815 Å / Origin y: 38.3597 Å / Origin z: -18.4699 Å
111213212223313233
T0.0146 Å20.0088 Å20.0029 Å2-0.0096 Å2-0.0009 Å2--0.0038 Å2
L1.4783 °2-0.2585 °2-0.3487 °2-1.267 °20.12 °2--1.1105 °2
S-0.0279 Å °-0.0076 Å °-0.0521 Å °-0.0524 Å °-0.0019 Å °-0.0278 Å °0.0895 Å °0.0315 Å °0.0298 Å °
Refinement TLS groupSelection: ALL

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