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- PDB-3exu: A glycoside hydrolase family 11 xylanase with an extended thumb region -

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Basic information

Entry
Database: PDB / ID: 3exu
TitleA glycoside hydrolase family 11 xylanase with an extended thumb region
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / beta-sandwich / Glycosidase / Xylan degradation
Function / homology
Function and homology information


endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process
Similarity search - Function
Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 ...Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase A / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsVandermarliere, E. / Pollet, A. / Strelkov, S.V. / Delcour, J.A. / Courtin, C.M.
CitationJournal: Proteins / Year: 2009
Title: Crystallographic and activity-based evidence for thumb flexibility and its relevance in glycoside hydrolase family 11 xylanases
Authors: Pollet, A. / Vandermarliere, E. / Lammertyn, J. / Strelkov, S.V. / Delcour, J.A. / Courtin, C.M.
History
DepositionOct 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase
B: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1495
Polymers40,7702
Non-polymers3793
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.910, 51.880, 84.730
Angle α, β, γ (deg.)90.00, 94.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endo-1,4-beta-xylanase


Mass: 20384.959 Da / Num. of mol.: 2 / Mutation: D11F, R122D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pEXP5-CT-xynA / Production host: Escherichia coli (E. coli)
References: UniProt: Q59254, UniProt: P18429*PLUS, endo-1,4-beta-xylanase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1M MES (pH 6.5), 30% PEG mme 5000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0011 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2007
RadiationMonochromator: Si 111 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0011 Å / Relative weight: 1
ReflectionResolution: 1.8→34 Å / Num. all: 34975 / Num. obs: 30673 / % possible obs: 87.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.076 / Net I/σ(I): 16
Reflection shellResolution: 1.81→1.91 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 4055 / Rsym value: 0.275 / % possible all: 80

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1bcx

1bcx


Resolution: 1.81→32.76 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.866 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23152 1541 5 %RANDOM
Rwork0.19051 ---
obs0.19259 29122 87.88 %-
all-34975 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.571 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å2-0.02 Å2
2---0.31 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.81→32.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2802 0 24 263 3089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212928
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.8814014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4135359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33823.603136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9215376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8581511
X-RAY DIFFRACTIONr_chiral_restr0.1110.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022325
X-RAY DIFFRACTIONr_nbd_refined0.1950.21206
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21921
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2236
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.220
X-RAY DIFFRACTIONr_mcbond_it0.5851.51783
X-RAY DIFFRACTIONr_mcangle_it1.04522827
X-RAY DIFFRACTIONr_scbond_it1.43231424
X-RAY DIFFRACTIONr_scangle_it1.8914.51185
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 100 -
Rwork0.246 1955 -
obs--80.12 %

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