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- PDB-7toi: Crystal structure of carbohydrate esterase PbeAcXE, in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7toi
TitleCrystal structure of carbohydrate esterase PbeAcXE, in complex with acetate
ComponentsSGNH hydrolase
KeywordsHYDROLASE / carbohydrate esterase / CE / Acetyl xylan esterases / xylan esterase / AcXE
Function / homology
Function and homology information


: / SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / SGNH hydrolase
Similarity search - Component
Biological speciesProlixibacter bellariivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.13 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 20, 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

Downloads & links

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Assembly

Deposited unit
A: SGNH hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7892
Polymers42,7301
Non-polymers591
Water11,854658
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.390, 42.560, 76.470
Angle α, β, γ (deg.)90.000, 108.300, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein SGNH hydrolase


Mass: 42729.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prolixibacter bellariivorans (bacteria)
Gene: PbJCM13498_02590 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Magic / References: UniProt: A0A5M4AV20
#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.: 658 / 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: 2.1 Å3/Da / Density % sol: 41.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 70 mM xylose, 0.1 M Tris pH 8.5, 0.2 M sodium acetate, and 30% (w/v) PEG4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.13→54.49 Å / Num. obs: 128873 / % possible obs: 98.1 % / Redundancy: 20.2 % / Biso Wilson estimate: 12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.023 / Net I/σ(I): 17.5
Reflection shellResolution: 1.13→1.16 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8881 / CC1/2: 0.657 / Rpim(I) all: 0.457 / % possible all: 91.7

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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: 1.13→54.49 Å / SU ML: 0.1075 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.6105
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1647 1997 1.55 %RANDOM
Rwork0.1528 126852 --
obs0.153 128849 98.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.58 Å2
Refinement stepCycle: LAST / Resolution: 1.13→54.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 4 658 3578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01263037
X-RAY DIFFRACTIONf_angle_d1.28034129
X-RAY DIFFRACTIONf_chiral_restr0.1058461
X-RAY DIFFRACTIONf_plane_restr0.0131538
X-RAY DIFFRACTIONf_dihedral_angle_d12.80041149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.160.28861330.2518430X-RAY DIFFRACTION91.45
1.16-1.190.23961320.22128784X-RAY DIFFRACTION95.81
1.19-1.220.19981570.20698831X-RAY DIFFRACTION96.53
1.22-1.260.19151240.18788946X-RAY DIFFRACTION97.4
1.26-1.310.19651520.17759010X-RAY DIFFRACTION98.08
1.31-1.360.17941430.17189044X-RAY DIFFRACTION98.31
1.36-1.420.17191430.1629078X-RAY DIFFRACTION98.49
1.42-1.50.17811410.1529097X-RAY DIFFRACTION99.22
1.5-1.590.16611500.14619177X-RAY DIFFRACTION99.26
1.59-1.720.15371410.14259170X-RAY DIFFRACTION99.64
1.72-1.890.16131430.14259227X-RAY DIFFRACTION99.87
1.89-2.160.14921440.13779286X-RAY DIFFRACTION99.99
2.16-2.720.15851440.14479314X-RAY DIFFRACTION99.99
2.72-54.490.15311500.14739458X-RAY DIFFRACTION99.85
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)
11.430136447110.4836078936460.6837542306140.8917043942920.295382165371.940274848750.0634218287952-0.018299023983-0.06455326346630.0212057986485-0.00657715610348-0.003415307794050.09074574386810.0559511421393-0.06465005791570.07827327667820.0166826879249-0.0006980567678460.0330904737591-0.003542658453560.091550350453129.1722142254.436686537343.1474557661
22.290733990290.845238674806-0.4884359804211.09504174043-0.219254804381.469130277790.02061834153640.0730595366009-0.167418112212-0.0184075558881-0.00407214472608-0.0565355347530.1016244402950.0667103209911-0.01386617321930.08366540106390.0194174997772-0.007872169782160.0754095032816-0.0118961952860.10855946340633.6508756487-1.5221612516539.2399361185
31.99699805179-0.06685185455820.2173343709830.623845954070.2289367451531.0962383180.04383726319020.15289221235-0.0195208175564-0.0695029555323-0.0210490477861-0.0305948096511-0.002485993245030.0715593709298-0.01845703722910.08580082893550.008930479350470.003436115583520.060615699766-0.0007748700803020.076916417957630.47721100955.4121913469137.8973555139
41.565226429560.2895949283730.01915978452941.8421449178-0.2171147529091.69993568284-0.0147478775383-0.09649752180060.0122169512670.0571499219340.0160254332939-0.138602666013-0.05252774772860.176590198363-0.01328546923150.09519839580130.007076460579570.006055747243020.095028457854-0.01992907359160.08265902860829.128565803713.920432603254.7104152919
53.40094123358-0.288841772342-0.4371621390631.291486862620.03005645036071.29267087679-0.0166137298523-0.128136177479-0.1428732008360.09474885760860.04361012011640.04058727805610.0918010170606-0.0253431353267-0.02128295019210.1090760406270.00197797692860.004333447083460.09679886818410.02162036447410.053519540472123.68326031695.9492392573361.4134767923
62.03121210719-0.6005691186540.1747059709821.20642306257-0.2932124437030.950507462194-0.0429673294811-0.270600989029-0.119843194530.1293730942120.08289936836350.1141394084490.0271287827019-0.0680656468813-0.03891751559330.1284697011830.02063508740520.0220061840420.1621735977870.003603569277150.07301751384817.06085121410.647839144467.5780913371
71.71860749004-0.166058680102-0.2512051719620.958148069234-0.115438350190.592850427567-0.0283129579774-0.2404693581930.0395275867690.1890532805780.0895786343910.0180934596375-0.04886304905580.00032650367138-0.06207669573850.1761153574690.04280334088140.01984161869390.198384875626-0.01757098864640.091758813656617.440856133717.807259842470.1151786551
81.819539849430.4681449035830.9415420858621.00744925066-0.05693140862352.224641441970.0638912219507-0.1061576647170.1536265771260.08512987777940.001288530764960.0356445626751-0.1248536452330.0488465219638-0.05633889267670.125822795366-0.007765334376470.01275249712910.0909916411778-0.03064317951730.099092421683621.206762642825.1766438458.8381268768
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 8 through 50 )8 - 501 - 43
22chain 'A' and (resid 51 through 105 )51 - 10544 - 98
33chain 'A' and (resid 106 through 175 )106 - 17599 - 168
44chain 'A' and (resid 176 through 240 )176 - 240169 - 233
55chain 'A' and (resid 241 through 272 )241 - 272234 - 265
66chain 'A' and (resid 273 through 316 )273 - 316266 - 309
77chain 'A' and (resid 317 through 346 )317 - 346310 - 339
88chain 'A' and (resid 347 through 386 )347 - 386340 - 379

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