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- PDB-7tog: Crystal structure of carbohydrate esterase PbeAcXE, apoenzyme -

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Basic information

Entry
Database: PDB / ID: 7tog
TitleCrystal structure of carbohydrate esterase PbeAcXE, apoenzyme
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
Biological speciesProlixibacter bellariivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 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 13, 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: SGNH hydrolase


Theoretical massNumber of molelcules
Total (without water)42,7301
Polymers42,7301
Non-polymers00
Water11,295627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.690, 42.580, 76.840
Angle α, β, γ (deg.)90.000, 108.290, 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 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Magic / References: UniProt: A0A5M4AV20
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
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: 1.35→28.78 Å / Num. obs: 77721 / % possible obs: 99.5 % / Redundancy: 8.9 % / Biso Wilson estimate: 18.11 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.035 / Net I/σ(I): 11.7
Reflection shellResolution: 1.35→1.39 Å / Redundancy: 7 % / Rmerge(I) obs: 1.282 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5628 / CC1/2: 0.562 / Rpim(I) all: 0.515 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.35→28.78 Å / SU ML: 0.1555 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.5305
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1795 3868 4.98 %RANDOM
Rwork0.1503 73832 --
obs0.1517 77700 99.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.59 Å2
Refinement stepCycle: LAST / Resolution: 1.35→28.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2910 0 0 627 3537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01713028
X-RAY DIFFRACTIONf_angle_d1.54724115
X-RAY DIFFRACTIONf_chiral_restr0.1268458
X-RAY DIFFRACTIONf_plane_restr0.0161535
X-RAY DIFFRACTIONf_dihedral_angle_d13.27491146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.27811020.29662592X-RAY DIFFRACTION98.43
1.37-1.380.2851320.26932595X-RAY DIFFRACTION98.77
1.38-1.40.31271370.26212594X-RAY DIFFRACTION98.49
1.4-1.420.25241440.25272597X-RAY DIFFRACTION98.77
1.42-1.440.25841260.24172603X-RAY DIFFRACTION98.59
1.44-1.460.26241530.23312624X-RAY DIFFRACTION99.18
1.46-1.490.23921310.21572578X-RAY DIFFRACTION98.98
1.49-1.510.23911400.2052632X-RAY DIFFRACTION99.28
1.51-1.540.20631570.19032581X-RAY DIFFRACTION98.92
1.54-1.560.21731450.17762603X-RAY DIFFRACTION99.03
1.56-1.590.21161560.17052632X-RAY DIFFRACTION99.93
1.59-1.630.22141260.16212637X-RAY DIFFRACTION99.96
1.63-1.660.16461220.15952650X-RAY DIFFRACTION99.96
1.66-1.70.17781510.15662622X-RAY DIFFRACTION99.96
1.7-1.740.19961370.1622642X-RAY DIFFRACTION99.75
1.74-1.790.21081270.16362649X-RAY DIFFRACTION100
1.79-1.840.18381150.1532647X-RAY DIFFRACTION99.89
1.84-1.90.18411360.14612652X-RAY DIFFRACTION99.82
1.9-1.970.16791360.14192636X-RAY DIFFRACTION99.96
1.97-2.050.14531560.14722666X-RAY DIFFRACTION99.96
2.05-2.140.16061330.13972644X-RAY DIFFRACTION99.96
2.14-2.260.1451400.1362656X-RAY DIFFRACTION100
2.26-2.40.15821580.13372644X-RAY DIFFRACTION99.96
2.4-2.580.16861270.1432657X-RAY DIFFRACTION99.96
2.58-2.840.19721510.15232671X-RAY DIFFRACTION100
2.84-3.250.19231720.14032652X-RAY DIFFRACTION99.82
3.25-4.10.14651260.12352696X-RAY DIFFRACTION99.93
4.1-28.780.17321320.14552780X-RAY DIFFRACTION99.73
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)
12.08727954179-0.1101972982230.1761098051780.979149214541-0.1609533984141.35037087510.0365316195898-0.0758610867981-0.1192247655040.0395102292524-0.01263478332630.04496047264440.0505091448071-0.102002284019-0.01674243707340.0960497290489-0.00610617726571-0.005675355878150.07218115917270.008664017705250.1048077573819.1744846066.1198085577969.7062051527
21.291677210510.336924836686-0.1707516024783.311876453630.3675948782221.824804521410.02468563657640.1241690038380.07081263214290.01379771525670.002058973492950.1256048574570.0337328893835-0.297458468497-0.0480773669770.1104768340520.01217911754380.009148198100260.1479427347540.02822148116310.090889141988921.697512960117.539764010956.7631973727
31.267339004370.271585351028-0.1107629149661.298375607850.07863847669441.16072227543-0.06952292733940.3113150397560.0423233802409-0.1688981506340.1103630793440.00134590630938-0.0658543696157-0.0524904166878-0.03634552291690.151800981846-0.01083700144630.002134213524670.2017186239150.01828333815420.099464180784928.757832208617.830662827646.4395245634
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 9 through 175 )9 - 1751 - 167
22chain 'A' and (resid 176 through 202 )176 - 202168 - 194
33chain 'A' and (resid 203 through 385 )203 - 385195 - 377

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