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- PDB-1mqq: THE CRYSTAL STRUCTURE OF ALPHA-D-GLUCURONIDASE FROM BACILLUS STEA... -

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Basic information

Entry
Database: PDB / ID: 1mqq
TitleTHE CRYSTAL STRUCTURE OF ALPHA-D-GLUCURONIDASE FROM BACILLUS STEAROTHERMOPHILUS T-1 COMPLEXED WITH GLUCURONIC ACID
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
alpha-D-glucopyranuronic acid / Xylan alpha-1,2-glucuronidase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.65 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
DepositionSep 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Feb 14, 2024Group: 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

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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)79,78613
Polymers78,5791
Non-polymers1,20712
Water11,818656
1
A: ALPHA-D-GLUCURONIDASE
hetero molecules

A: ALPHA-D-GLUCURONIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,57326
Polymers157,1582
Non-polymers2,41424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)74.092, 74.092, 331.863
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-1348-

HOH

21A-1350-

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)
Strain: T-1 / Gene: AGUA / Plasmid: PET9D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8VVD2, EC: 3.2.1.139
#2: Sugar ChemComp-GCU / alpha-D-glucopyranuronic acid / alpha-D-glucuronic acid / D-glucuronic acid / glucuronic acid


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGlcpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
a-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / 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: 2.88 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 12% isopropanol, 14% PEG 4K, 0.1M Na-citrate, pH 5.0, 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 - B4 / 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: 1.65→40 Å / Num. obs: 111221 / % possible obs: 98.9 % / Redundancy: 10 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.9
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 10 % / Rmerge(I) obs: 0.452 / Num. unique all: 4995 / % possible all: 91

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: AB INITIO
Starting model: PDB CODE 1K9D

1k9d


Resolution: 1.65→40 Å / Num. parameters: 25802 / Num. restraintsaints: 24044 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 5353 4.8 %RANDOM
Rwork0.1851 ---
all0.1853 111221 --
obs-111221 98.9 %-
Refine analyzeLuzzati coordinate error obs: 0.15 Å / Num. disordered residues: 44 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 6237.05
Refinement stepCycle: LAST / Resolution: 1.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5510 0 79 656 6245
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0262
X-RAY DIFFRACTIONs_zero_chiral_vol0.042
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.053
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.063
X-RAY DIFFRACTIONs_approx_iso_adps0

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