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- PDB-8air: Crystal structure of cutinase RgCutII from Rhizobacter gummiphilus -

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Basic information

Entry
Database: PDB / ID: 8air
TitleCrystal structure of cutinase RgCutII from Rhizobacter gummiphilus
ComponentsRgCutII
KeywordsHYDROLASE / PET / cutinase / ester bond / cleavage
Function / homologyAlpha/Beta hydrolase fold / ACETATE ION / Uncharacterized protein
Function and homology information
Biological speciesRhizobacter gummiphilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 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 / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _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

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Assembly

Deposited unit
A: RgCutII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8003
Polymers30,6821
Non-polymers1182
Water6,017334
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)63.127, 63.127, 222.746
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-645-

HOH

21A-658-

HOH

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Components

#1: Protein RgCutII


Mass: 30681.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobacter gummiphilus (bacteria) / Gene: A4W93_03190 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1W6L438
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.09 Å3/Da / Density % sol: 41.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 1 M sodium acetate

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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: 1.08→49.08 Å / Num. obs: 112681 / % possible obs: 99.4 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.024 / Net I/σ(I): 11.7
Reflection shellResolution: 1.08→1.1 Å / Redundancy: 6 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5357 / CC1/2: 0.555 / Rpim(I) all: 0.44 / % possible all: 96.3

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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: 1.08→49.076 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.519 / SU ML: 0.033 / Cross valid method: FREE R-VALUE / ESU R: 0.036 / ESU R Free: 0.037
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.214 5265 5.041 %
Rwork0.1978 99186 -
all0.199 --
obs-104451 92.16 %
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: 12.965 Å2
Baniso -1Baniso -2Baniso -3
1-0.466 Å20.233 Å20 Å2
2--0.466 Å2-0 Å2
3----1.511 Å2
Refinement stepCycle: LAST / Resolution: 1.08→49.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 8 334 2262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0112019
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161786
X-RAY DIFFRACTIONr_angle_refined_deg1.8411.6382764
X-RAY DIFFRACTIONr_angle_other_deg0.6381.5444177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2525271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.6861013
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14610300
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.661078
X-RAY DIFFRACTIONr_chiral_restr0.0970.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022354
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02418
X-RAY DIFFRACTIONr_nbd_refined0.2380.2393
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21718
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21021
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21049
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2236
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1330.212
X-RAY DIFFRACTIONr_nbd_other0.1640.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2450.241
X-RAY DIFFRACTIONr_mcbond_it0.8420.7411041
X-RAY DIFFRACTIONr_mcbond_other0.8360.7391039
X-RAY DIFFRACTIONr_mcangle_it1.3211.1081301
X-RAY DIFFRACTIONr_mcangle_other1.3221.1121302
X-RAY DIFFRACTIONr_scbond_it1.3760.896978
X-RAY DIFFRACTIONr_scbond_other1.3760.897979
X-RAY DIFFRACTIONr_scangle_it2.0461.291455
X-RAY DIFFRACTIONr_scangle_other2.0461.2911456
X-RAY DIFFRACTIONr_lrange_it4.85116.5082461
X-RAY DIFFRACTIONr_lrange_other4.56910.8262326
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
1.08-1.1080.4143660.41469040.41482320.8440.8588.31390.403
1.108-1.1380.393580.37969610.3880210.8760.87991.2480.363
1.138-1.1710.3593800.35567770.35578190.9020.90391.53340.333
1.171-1.2070.3363300.32866380.32975550.8970.91992.23030.304
1.207-1.2470.3473400.30964700.31173980.9160.93192.05190.28
1.247-1.2910.3073290.29762670.29871270.9350.9492.54950.264
1.291-1.3390.3083070.27561030.27669020.9380.95192.87160.238
1.339-1.3940.2843430.25658320.25866600.9510.95692.71770.22
1.394-1.4560.2523040.23555780.23563890.9590.96692.06450.198
1.456-1.5270.2463180.20953240.21161130.9650.97392.29510.176
1.527-1.6090.2092770.19651260.19758690.9750.97692.060.165
1.609-1.7070.2122490.18948530.1955560.9710.97891.82870.16
1.707-1.8250.1762370.17444990.17452160.980.98190.79750.152
1.825-1.9710.1632400.16242720.16248970.9840.98492.1380.145
1.971-2.1580.1852040.1639810.16145130.9790.98492.73210.149
2.158-2.4130.211920.15636790.15841340.9740.98593.63810.151
2.413-2.7850.161590.15432870.15436790.9830.98593.66680.155
2.785-3.4080.1551500.15228680.15231590.9870.98695.53660.16
3.408-4.8080.1471130.14623320.14625180.9860.98897.10090.163
4.808-49.0760.209690.17414270.17515360.9730.9897.39580.191
Refinement TLS params.Method: refined / Origin x: 21.5331 Å / Origin y: -15.6011 Å / Origin z: 1.0352 Å
111213212223313233
T0.0143 Å20.0054 Å2-0.0069 Å2-0.0042 Å20.0004 Å2--0.0616 Å2
L0.8408 °20.1578 °20.0635 °2-0.8759 °20.349 °2--1.0906 °2
S0.0114 Å °-0.0317 Å °-0.0196 Å °0.0436 Å °0.0081 Å °-0.0081 Å °0.0389 Å °0.0348 Å °-0.0195 Å °
Refinement TLS groupSelection: ALL

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