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- PDB-2exk: Structure of the family43 beta-Xylosidase E187G from geobacillus ... -

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Basic information

Entry
Database: PDB / ID: 2exk
TitleStructure of the family43 beta-Xylosidase E187G from geobacillus stearothermophilus in complex with xylobiose
Componentsbeta-D-xylosidase
KeywordsHYDROLASE / glykosidase / hydrolsase / xylosidase / family43 / xylose
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Jelly Rolls - #200 ...: / Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta-xylosidase / :
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBrux, C. / Niefind, K. / Shallom-Shezifi, D. / Shoham, Y. / Schomburg, D.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: The Structure of an Inverting GH43 beta-Xylosidase from Geobacillus stearothermophilus with its Substrate Reveals the Role of the Three Catalytic Residues.
Authors: Brux, C. / Ben-David, A. / Shallom-Shezifi, D. / Leon, M. / Niefind, K. / Shoham, G. / Shoham, Y. / Schomburg, D.
#1: Journal: To be Published
Title: Crystallization and preliminary crystallographic analysis of a family 43 ?-D-xylosidase from Geobacillus stearothermophilus T-6
#2: Journal: Biochemistry / Year: 2005
Title: Biochemical Characterization and Identification of the Catalytic Residues of a Family 43 beta-D-Xylosidase from Geobacillus stearothermophilus T-6
History
DepositionNov 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / diffrn_source / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: beta-D-xylosidase
B: beta-D-xylosidase
C: beta-D-xylosidase
D: beta-D-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,83219
Polymers247,5894
Non-polymers2,24315
Water19,6541091
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16740 Å2
ΔGint-47 kcal/mol
Surface area70060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.870, 139.870, 232.025
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a tetramer

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
beta-D-xylosidase


Mass: 61897.227 Da / Num. of mol.: 4 / Mutation: E187G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: pET9d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q68HB3, UniProt: Q09LX0*PLUS, xylan 1,4-beta-xylosidase
#2: Polysaccharide
alpha-D-xylopyranose-(1-4)-alpha-D-xylopyranose


Type: oligosaccharide / Mass: 282.245 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-4DXylpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a212h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 1102 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1091 / 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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 17% PEG 6000, 0.1M MES, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8048 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 26, 2005
RadiationMonochromator: Bent mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8048 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 117206 / Num. obs: 116620 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.23 Å / % possible all: 97.8

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Phasing

Phasing MRRfactor: 37.5 / Cor.coef. Fo:Fc: 64.8 / Cor.coef. Io to Ic: 64.8
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→2.23 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 13.073 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.304 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 5803 5 %RANDOM
Rwork0.185 ---
all0.188 117206 --
obs0.188 115793 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.609 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2---0.7 Å20 Å2
3---1.41 Å2
Refinement stepCycle: LAST / Resolution: 2.2→2.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17484 0 140 1091 18715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02118196
X-RAY DIFFRACTIONr_angle_refined_deg1.341.94324796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.57852128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0923.19928
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.658152792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.99215120
X-RAY DIFFRACTIONr_chiral_restr0.1030.22563
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214264
X-RAY DIFFRACTIONr_nbd_refined0.1890.29013
X-RAY DIFFRACTIONr_nbtor_refined0.3090.211997
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.21719
X-RAY DIFFRACTIONr_metal_ion_refined0.140.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.213
X-RAY DIFFRACTIONr_mcbond_it0.431.510877
X-RAY DIFFRACTIONr_mcangle_it0.752217188
X-RAY DIFFRACTIONr_scbond_it1.0538553
X-RAY DIFFRACTIONr_scangle_it1.6824.57608
LS refinement shellResolution: 2.2→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 401 -
Rwork0.232 7851 -
obs-8252 97.8 %

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