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- PDB-7tok: Crystal structure of the CBM domain of carbohydrate esterase FjoAcXE -

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Basic information

Entry
Database: PDB / ID: 7tok
TitleCrystal structure of the CBM domain of carbohydrate esterase FjoAcXE
ComponentsAcetylxylan esterase I
KeywordsHYDROLASE / carbohydrate esterase / CE / Acetyl xylan esterases / xylan esterase / AcXE
Function / homology: / acetylxylan esterase / acetylxylan esterase activity / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Acetylxylan esterase I
Function and homology information
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsStogios, P.J. / Skarina, T. / Di Leo, R. / Jurak, E. / Master, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Molecules / Year: 2022
Title: Elucidating Sequence and Structural Determinants of Carbohydrate Esterases for Complete Deacetylation of Substituted Xylans.
Authors: Penttinen, L. / Kouhi, V. / Faure, R. / Skarina, T. / Stogios, P. / Master, E. / Jurak, E.
History
DepositionJan 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Acetylxylan esterase I
B: Acetylxylan esterase I


Theoretical massNumber of molelcules
Total (without water)32,7802
Polymers32,7802
Non-polymers00
Water18010
1
A: Acetylxylan esterase I


Theoretical massNumber of molelcules
Total (without water)16,3901
Polymers16,3901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acetylxylan esterase I


Theoretical massNumber of molelcules
Total (without water)16,3901
Polymers16,3901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.084, 120.964, 86.645
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-206-

HOH

21B-207-

HOH

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Components

#1: Protein Acetylxylan esterase I


Mass: 16389.973 Da / Num. of mol.: 2 / Mutation: L62 and V113 mutated to selenomethionine
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: axeA / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Magic / References: UniProt: A0A5P6A8B9, acetylxylan esterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1 M ammonium sulfate, 0.6 M sodium citrate and 0.1 M calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.45→60.48 Å / Num. obs: 11980 / % possible obs: 99.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.026 / Net I/σ(I): 18.6
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.55 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1725 / CC1/2: 0.519 / Rpim(I) all: 0.745 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
Aimlessdata scaling
HKL-3000phasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.45→43.32 Å / SU ML: 0.5616 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.7322
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2835 560 4.7 %RANDOM
Rwork0.2297 11356 --
obs0.2323 11916 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.47 Å2
Refinement stepCycle: LAST / Resolution: 2.45→43.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 0 10 1983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00452005
X-RAY DIFFRACTIONf_angle_d0.96572706
X-RAY DIFFRACTIONf_chiral_restr0.0537323
X-RAY DIFFRACTIONf_plane_restr0.0069346
X-RAY DIFFRACTIONf_dihedral_angle_d19.9058735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.690.45251300.39512782X-RAY DIFFRACTION98.75
2.69-3.080.36831470.37292807X-RAY DIFFRACTION99.86
3.08-3.880.33971380.26852826X-RAY DIFFRACTION99.83
3.89-43.320.23241450.17912941X-RAY DIFFRACTION99.2
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)
18.333576402393.62013187927-2.694296461094.79008142571-3.008584152856.798329704810.0311931200934-0.241774111177-0.231146893191-1.01365035655-0.2931682174160.6363996172460.5674481796340.01787173525820.1226536124660.7735795258770.2155006008740.01166308106880.711132967288-0.0295374035230.51645290526314.235054896825.247551492271.2385495084
29.36296077309-0.614843500375-7.876136134117.02573333389-2.537402282927.52704825950.3428709362460.571087609278-0.7009217871-0.501363803248-0.9376320519440.6698937061620.099108454393-0.2411408922740.6126146272430.762364961190.294791749914-0.1660732906090.827415364173-0.2454833351430.4499519434366.402977152227.380079487574.3489114205
34.642283304256.65085361316-2.652004423112.02508999978-2.362584976995.60171036581-1.448210541620.753817308312-0.1001573486990.8255070962220.206422635161-4.171179058661.569294333353.964578513520.0994753176461.13057731270.553439539747-0.2546897541681.339546708830.1070617400011.100654401524.423873271819.463308054973.8508264223
45.790797897852.9785118716-6.431570417937.98085942258-4.433005954476.988859041041.3814628361-0.02782146391190.9054299243461.20367186183-0.5873961171980.98787991732-0.1244889829150.694264036868-0.7201758995020.9300639831880.227169436882-0.1614595757090.669949126113-0.1683617541770.56096879147.3092697218132.715912006678.3580769715
58.170168092561.61222053647-3.318961893216.14674363257-1.742023276877.73801266945-0.416694957466-0.566349727844-0.8927877411140.072210145936-0.516599373033-0.1247811118880.6497479499330.5429341687440.8643096472530.6067324708110.209853496868-0.04487793780890.6339770225830.06764537666250.46081605440215.718649587922.680050675674.9767033955
64.38960307814-4.84454590472-5.228408777245.369289559565.760692831726.189950643120.5605281462310.0197224910843-1.37755576646-4.59126535434-0.004625693142451.61768299256-0.429916602626-1.69045836804-0.6452108083681.44896252856-0.00156826550971-0.3172643959121.2941445214-0.2419498130791.196681874077.7655370610515.866925733269.1965106387
73.554151519013.52119125993-3.442720950314.29343017709-3.870326595933.563866685760.881562626482.286076719220.545204590839-2.18657456463-0.1507309967960.255245243712-0.796555987995-0.289920945632-0.7034856496581.180243415510.3407751074080.1350420816920.927761532346-0.04348795109310.80981509853913.300229856336.22605470568.105765388
89.89307113617-2.812427999641.188305228725.821150155073.270792793635.091453882210.5703579510250.1017869791321.5541178720.366273155077-0.883870188011-0.2892452979931.1413388240.2756406149220.005237952496860.604714589902-0.1459231845250.03435029821650.6252497169230.07056437277590.8667225263648.360192591654.34720271454.5480759692
95.92052405674-0.1244324923966.199863566933.18170077172-1.027787150015.91949423436-0.734406809385-1.182835465060.4872106002351.06516391817-0.1129206258290.4898392025590.133840002158-1.121286023070.707384431720.762287146961-0.02986538855850.1854855927650.76168000388-0.1777178258860.618706973037.3559651102342.647564590458.1571978812
104.75619095382-3.74997296413-3.32917668567.60618869030.4519670972923.342747145370.2133594773750.5133649915850.319556136736-0.363791183749-0.434512849927-1.089837065990.09427295548260.7408721675340.3186052860450.607736447029-0.09679720163190.02885145914060.7068160831170.1132981596150.54004527686913.056379526547.411149715248.2198265117
114.49911699027-4.593311077441.329428832714.62698588973-1.557732528182.425342082530.385873210771-1.86067382938-1.49931752450.2626120047020.374304387221.792538726910.172281448416-0.59440264658-0.591516773680.733130039866-0.1420616897320.1547293573920.856924394130.09150814195080.686555101289-0.75225281391740.242699698455.3025803003
126.16986933699-3.799499831634.01583729088.02500490678-3.552644992225.60430953089-0.04802145234560.7000701173630.9540008602650.376559006054-0.486543686608-0.407211593421-0.4487180651990.512117388510.5611821518210.536891527031-0.05841920585640.1175597535220.5686167296820.0716243024240.64527291143613.412813044850.377785301551.8774985955
139.76606474399-4.685474318086.727020726487.7354570243-5.035151830047.11652075722-1.26836003004-2.66430520583-0.8736021991212.72977020838-1.59903917381-1.86725910874-1.429081780630.05888374570931.847570685291.314990809370.03594743619080.4836440571140.897569309983-0.1939932737550.782818279817.8201060664458.612402441157.5554582165
143.19032946938-2.27545456776-0.7792831858984.98621376854-0.2371701165011.87372901553-0.00855522224499-1.25938600153-1.598246207022.46601952853-0.3001680739471.015053255130.964084783266-0.3685157708440.3154608748580.628294130687-0.3448593786080.01576207117320.965218975232-0.08275693268190.87651684290812.033374140837.35777674358.8856708014
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 41 through 60 )AA41 - 601 - 20
22chain 'A' and (resid 61 through 82 )AA61 - 8221 - 42
33chain 'A' and (resid 83 through 93 )AA83 - 9343 - 53
44chain 'A' and (resid 94 through 114 )AA94 - 11454 - 74
55chain 'A' and (resid 115 through 165 )AA115 - 16575 - 113
66chain 'A' and (resid 166 through 177 )AA166 - 177114 - 122
77chain 'A' and (resid 178 through 185 )AA178 - 185123 - 130
88chain 'B' and (resid 40 through 53 )BB40 - 531 - 14
99chain 'B' and (resid 54 through 72 )BB54 - 7215 - 33
1010chain 'B' and (resid 73 through 104 )BB73 - 10434 - 65
1111chain 'B' and (resid 105 through 114 )BB105 - 11466 - 75
1212chain 'B' and (resid 115 through 164 )BB115 - 16476 - 113
1313chain 'B' and (resid 165 through 177 )BB165 - 177114 - 122
1414chain 'B' and (resid 178 through 185 )BB178 - 185123 - 130

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