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- PDB-2z79: High resolution crystal structure of a glycoside hydrolase family... -

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Basic information

Entry
Database: PDB / ID: 2z79
TitleHigh resolution crystal structure of a glycoside hydrolase family 11 xylanase of Bacillus subtilis
ComponentsEndo-1,4-beta-xylanase A
KeywordsHYDROLASE / glycoside hydrolase / xylanase / Glycosidase / Xylan degradation
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / 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, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / 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
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsVandermarliere, E. / Bourgois, T.M. / Strelkov, S.V. / Delcour, J.A. / Courtin, C.M. / Rabijns, A.
CitationJournal: Biochem.J. / Year: 2008
Title: Crystallographic analysis shows substrate binding at the -3 to +1 active-site subsites and at the surface of glycoside hydrolase family 11 endo-1,4-beta-xylanases.
Authors: Vandermarliere, E. / Bourgois, T.M. / Rombouts, S. / Van Campenhout, S. / Volckaert, G. / Strelkov, S.V. / Delcour, J.A. / Rabijns, A. / Courtin, C.M.
History
DepositionAug 16, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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 A
B: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,41110
Polymers40,6742
Non-polymers7378
Water6,305350
1
A: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7055
Polymers20,3371
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7055
Polymers20,3371
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.870, 63.059, 122.435
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endo-1,4-beta-xylanase A / Xylanase A / 1 / 4- beta-D-xylan xylanohydrolase A


Mass: 20336.943 Da / Num. of mol.: 2 / Mutation: E172A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P18429, endo-1,4-beta-xylanase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 1.94 Å3/Da / Density % sol: 36.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M imidazole pH 6.5, 1.0M sodium acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9918 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 12, 2006
RadiationMonochromator: Fixed exit double crystal Si [111], horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9918 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. all: 73641 / Num. obs: 70534 / % possible obs: 89.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.4 / Rsym value: 0.086 / Net I/σ(I): 18
Reflection shellResolution: 1.3→1.32 Å / Mean I/σ(I) obs: 5.7 / Num. unique all: 3109 / Rsym value: 0.165 / % possible all: 80.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BCX

1bcx


Resolution: 1.3→22.83 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.449 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1762 3552 5 %RANDOM
Rwork0.15738 ---
obs0.15833 66927 89.62 %-
all-66927 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.19 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.3→22.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2876 0 48 350 3274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213072
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.171.8894222
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1545392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32423.429140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.33115400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5411514
X-RAY DIFFRACTIONr_chiral_restr0.0720.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022430
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.21367
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22064
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2304
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6311.51857
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03422983
X-RAY DIFFRACTIONr_scbond_it1.49931485
X-RAY DIFFRACTIONr_scangle_it1.8794.51226
X-RAY DIFFRACTIONr_rigid_bond_restr0.99333342
X-RAY DIFFRACTIONr_sphericity_free2.713350
X-RAY DIFFRACTIONr_sphericity_bonded1.9132971
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 240 -
Rwork0.204 4312 -
obs--79.59 %

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