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- PDB-1l8n: The 1.5A crystal structure of alpha-D-glucuronidase from Bacillus... -

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Entry
Database: PDB / ID: 1l8n
TitleThe 1.5A crystal structure of alpha-D-glucuronidase from Bacillus stearothermophilus T-1, complexed with 4-O-methyl-glucuronic acid and xylotriose
ComponentsALPHA-D-GLUCURONIDASE
KeywordsHYDROLASE
Function / homology
Function and homology information


xylan alpha-1,2-glucuronosidase / xylan alpha-1,2-glucuronosidase activity / alpha-glucuronidase activity / xylan catabolic process / extracellular region
Similarity search - Function
Alpha-d-glucuronidase, C-terminal Domain / Alpha-glucuronidase, C-terminal domain / Alpha glucuronidase, N-terminal / Glycosyl hydrolase family 67, C-terminal / Glycosyl hydrolase family 67, catalytic domain / Alpha glucuronidase / Alpha-glucuronidase, C-terminal domain superfamily / Glycosyl hydrolase family 67 N-terminus / Glycosyl hydrolase family 67 C-terminus / Glycosyl hydrolase family 67 middle domain ...Alpha-d-glucuronidase, C-terminal Domain / Alpha-glucuronidase, C-terminal domain / Alpha glucuronidase, N-terminal / Glycosyl hydrolase family 67, C-terminal / Glycosyl hydrolase family 67, catalytic domain / Alpha glucuronidase / Alpha-glucuronidase, C-terminal domain superfamily / Glycosyl hydrolase family 67 N-terminus / Glycosyl hydrolase family 67 C-terminus / Glycosyl hydrolase family 67 middle domain / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
4beta-beta-xylobiose / 4-O-methyl-beta-D-glucopyranuronic acid / : / Xylan alpha-1,2-glucuronidase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.5 Å
AuthorsGolan, G. / Shallom, D. / Teplitsky, A. / Zaide, G. / Shulami, S. / Baasov, T. / Stojanoff, V. / Thompson, A. / Shoham, Y. / Shoham, G.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structures of Geobacillus stearothermophilus {alpha}-Glucuronidase Complexed with Its Substrate and Products: MECHANISTIC IMPLICATIONS.
Authors: Golan, G. / Shallom, D. / Teplitsky, A. / Zaide, G. / Shulami, S. / Baasov, T. / Stojanoff, V. / Thompson, A. / Shoham, Y. / Shoham, G.
History
DepositionMar 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / 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_alt_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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 600HETEROGEN THE PRODUCT IS XYLOTRIOSE. IN THE ENTRY, XYP 702 AND XYP 703 ARE COVALENTLY BOUND. THE ...HETEROGEN THE PRODUCT IS XYLOTRIOSE. IN THE ENTRY, XYP 702 AND XYP 703 ARE COVALENTLY BOUND. THE THIRD XYLOSE IS NOT MODELED DUE TO LACK OF FIXED POSITION AND CLEAR DENSITY. THE BOND BETWEEN GCW 701 AND XYP 702 WAS BROKEN BY THE ENZYME. ALSO, XYP 702 AND GOL 763 OCCUPY THE SAME SPACE AND EACH HAVE HALF OCCUPANCY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-D-GLUCURONIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,35917
Polymers78,5791
Non-polymers1,78016
Water12,016667
1
A: ALPHA-D-GLUCURONIDASE
hetero molecules

A: ALPHA-D-GLUCURONIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,71834
Polymers157,1582
Non-polymers3,55932
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)73.946, 73.946, 331.341
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1078-

HOH

21A-1146-

HOH

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Components

#1: Protein ALPHA-D-GLUCURONIDASE


Mass: 78579.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: AGUA / Plasmid: PET9D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: GenBank: 16930794, UniProt: Q8VVD2*PLUS, EC: 3.2.1.139
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 282.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylobiose
DescriptorTypeProgram
DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a212h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-GCW / 4-O-methyl-beta-D-glucopyranuronic acid / 4-O-METHYL-BETA-D-GLUCURONIC ACID / 4-O-methyl-D-glucuronic acid / 4-O-methyl-glucuronic acid


Type: D-saccharide, beta linking / Mass: 208.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C7H12O7
IdentifierTypeProgram
b-D-GlcpA4OMeIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 667 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M NA-CITRATE PH 5.0, 14% PEG 4000, 12% ISO-PROPANOL, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: BRANDEIS / Detector: CCD / Date: Jul 12, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. obs: 145976 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 15 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.8
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.399 / Num. unique all: 6525 / % possible all: 90.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
SHELXL-97refinement
CNSphasing
RefinementMethod to determine structure: AB INITIO
Starting model: pdb code 1k9d

1k9d


Resolution: 1.5→10 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1721 7157 -RANDOM
Rwork0.1395 ---
all-141046 --
obs-141046 95.1 %-
Refine analyzeNum. disordered residues: 42
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5488 0 117 667 6272
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg2.13

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