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- PDB-8c65: Crystal structure of cutinase AdCut from Acidovorax delafieldii (... -

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Basic information

Entry
Database: PDB / ID: 8c65
TitleCrystal structure of cutinase AdCut from Acidovorax delafieldii (PBS depolymerase)
ComponentsPBS(A) depolymerase
KeywordsHYDROLASE / cutinase / PET / PBS
Function / homologyDienelactone hydrolase / Dienelactone hydrolase family / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / PBS(A) depolymerase
Function and homology information
Biological speciesAcidovorax delafieldii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.491 Å
AuthorsZahn, M. / Clark, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)Research England E3 United Kingdom
CitationJournal: Acs Omega / Year: 2024
Title: Understanding the Catalytic Efficiency of Two Polyester Degrading Enzymes: An Experimental and Theoretical Investigation.
Authors: Clark, M. / Tornesakis, K. / Konig, G. / Zahn, M. / Lichtenstein, B.R. / Pickford, A.R. / Cox, P.A.
History
DepositionJan 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.2Nov 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Nov 27, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PBS(A) depolymerase
B: PBS(A) depolymerase


Theoretical massNumber of molelcules
Total (without water)58,7572
Polymers58,7572
Non-polymers00
Water7,296405
1
A: PBS(A) depolymerase


Theoretical massNumber of molelcules
Total (without water)29,3781
Polymers29,3781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PBS(A) depolymerase


Theoretical massNumber of molelcules
Total (without water)29,3781
Polymers29,3781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.798, 96.430, 58.525
Angle α, β, γ (deg.)90.000, 111.033, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ASN / End label comp-ID: ASN / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 42 - 304 / Label seq-ID: 1 - 263

Dom-ID
1
2

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

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Components

#1: Protein PBS(A) depolymerase


Mass: 29378.479 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidovorax delafieldii (bacteria) / Gene: pbsA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RR62
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O
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: 2.05 Å3/Da / Density % sol: 40.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG 3350, 0.2 M ammonium citrate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.491→54.626 Å / Num. obs: 39403 / % possible obs: 78.1 % / Redundancy: 6.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.08 / Net I/σ(I): 7.1
Reflection shellResolution: 1.491→1.594 Å / Redundancy: 7 % / Rmerge(I) obs: 1.262 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1971 / CC1/2: 0.529 / Rpim(I) all: 0.508 / % possible all: 65.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.491→54.626 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.252 / SU ML: 0.079 / Cross valid method: FREE R-VALUE / ESU R: 0.157 / ESU R Free: 0.14
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2147 1897 4.814 %
Rwork0.1753 37505 -
all0.177 --
obs-39402 51.098 %
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: 10.792 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0 Å20.092 Å2
2--0.047 Å20 Å2
3----0.222 Å2
Refinement stepCycle: LAST / Resolution: 1.491→54.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3976 0 0 405 4381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0114114
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163516
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.6455618
X-RAY DIFFRACTIONr_angle_other_deg0.5491.5498254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0825543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.239534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92210614
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.63210180
X-RAY DIFFRACTIONr_chiral_restr0.0770.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02844
X-RAY DIFFRACTIONr_nbd_refined0.2250.2919
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.23475
X-RAY DIFFRACTIONr_nbtor_refined0.180.22103
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22063
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.2334
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.212
X-RAY DIFFRACTIONr_nbd_other0.1650.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2240.235
X-RAY DIFFRACTIONr_mcbond_it0.7960.782122
X-RAY DIFFRACTIONr_mcbond_other0.7920.7792122
X-RAY DIFFRACTIONr_mcangle_it1.361.1612654
X-RAY DIFFRACTIONr_mcangle_other1.3641.1632655
X-RAY DIFFRACTIONr_scbond_it1.1090.9021992
X-RAY DIFFRACTIONr_scbond_other1.1050.91991
X-RAY DIFFRACTIONr_scangle_it1.7431.3142954
X-RAY DIFFRACTIONr_scangle_other1.7421.3152955
X-RAY DIFFRACTIONr_lrange_it3.85414.934962
X-RAY DIFFRACTIONr_lrange_other3.72211.9074868
X-RAY DIFFRACTIONr_ncsr_local_group_10.0680.059060
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.068370.0501
12AX-RAY DIFFRACTIONLocal ncs0.068370.0501
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
1.491-1.530.341130.274050.27257060.9370.9557.32560.261
1.53-1.5710.246500.2628760.26155210.9590.95816.77230.255
1.571-1.6170.262700.23512400.23753760.9510.96224.36760.227
1.617-1.6670.241850.24215520.24252670.9610.9631.08030.23
1.667-1.7210.252930.23117260.23250530.9540.96335.99840.216
1.721-1.7820.282910.23618440.23848860.9530.96339.60290.22
1.782-1.8490.2681020.22119300.22347660.9530.96942.63530.202
1.849-1.9240.274510.2397940.24145490.9550.96218.57550.212
1.924-2.010.296650.21715470.2243860.9520.97136.75330.186
2.01-2.1080.274720.2115780.21341810.950.9739.46420.182
2.108-2.2220.2021530.18434050.18539800.9710.97889.3970.156
2.222-2.3560.2211580.18927990.19137590.9650.97678.66450.156
2.356-2.5180.2321980.18133500.18435550.9610.97899.80310.153
2.518-2.720.2111200.17225750.17433010.9750.98281.64190.147
2.72-2.9780.1891390.14929060.15130470.9760.98699.93440.135
2.978-3.3290.2161100.15326540.15627640.9680.9851000.143
3.329-3.8410.1911120.15922540.1624200.9760.98497.76860.15
3.841-4.6990.179940.1416740.14220760.9820.98885.16380.137
4.699-6.6210.179840.14515320.14616160.9830.9881000.143
6.621-54.6260.192370.1638640.1649010.9830.9791000.168
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)
10.408-0.0197-0.00480.6894-0.01980.7747-0.0056-0.0184-0.0130.01020.00830.00580.01090.0016-0.00260.00840.0026-0.0010.0034-0.0050.0157-0.18540.3388.6597
20.64840.0903-0.24140.7044-0.11230.69330.00330.00830.00650.0094-0.00370.0172-0.01230.00090.00040.00790.003-0.00280.0033-0.00510.0095-4.908127.410520.7016
Refinement TLS groupSelection: ALL

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