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- PDB-1k9e: Crystal structure of a mutated family-67 alpha-D-glucuronidase (E... -

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Basic information

Entry
Database: PDB / ID: 1k9e
TitleCrystal structure of a mutated family-67 alpha-D-glucuronidase (E285N) from Bacillus stearothermophilus T-6, complexed with 4-O-methyl-glucuronic acid
Componentsalpha-D-glucuronidase
KeywordsHYDROLASE
Function / homology
Function and homology information


glucuronoxylan catabolic process / 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
4-O-methyl-alpha-D-glucopyranuronic acid / Xylan alpha-(1->2)-glucuronosidase / Xylan alpha-1,2-glucuronidase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.85 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
DepositionOct 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 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.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 27, 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 1.5Aug 16, 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

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Assembly

Deposited unit
A: alpha-D-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,78413
Polymers78,5631
Non-polymers1,22112
Water8,701483
1
A: alpha-D-glucuronidase
hetero molecules

A: alpha-D-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,56926
Polymers157,1272
Non-polymers2,44224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)73.576, 73.576, 330.568
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein alpha-D-glucuronidase


Mass: 78563.258 Da / Num. of mol.: 1 / Mutation: E285N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: T6 / Gene: AGUA / Plasmid: pET9d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q8VVD2, UniProt: Q09LY5*PLUS, EC: 3.2.1.139
#2: Sugar ChemComp-GCV / 4-O-methyl-alpha-D-glucopyranuronic acid / 4-O-METHYL-ALPHA-D-GLUCURONIC ACID / 4-O-methyl-D-glucuronic acid / 4-O-methyl-glucuronic acid


Type: D-saccharide, alpha linking / Mass: 208.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C7H12O7
IdentifierTypeProgram
a-D-GlcpA4OMeIUPAC CARBOHYDRATE SYMBOLPDB-CARE 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.: 483 / 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: 2.85 Å3/Da / Density % sol: 56.78 %
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
Crystal grow
*PLUS
Temperature: 20 ℃ / PH range low: 5.5 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlenzyme1drop
214 %(w/v)PEG40001reservoir
312 %(v/v)isopropyl alcohol1reservoir
40.1 Msodium citrate1reservoirpH5.0-5.5

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9766 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 29, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9766 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 72670 / % possible obs: 92.1 % / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.6
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 0.234 / % possible all: 63.1
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 354446
Reflection shell
*PLUS
% possible obs: 63.1 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: AB INITIO PHASING
Starting model: PDB ENTRY 1K9D

1k9d


Resolution: 1.85→36.03 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 192936.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.218 6967 10.1 %RANDOM
Rwork0.193 ---
obs0.193 68943 92.1 %-
all-72670 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.0392 Å2 / ksol: 0.374165 e/Å3
Displacement parametersBiso mean: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.15 Å20 Å20 Å2
2--3.15 Å20 Å2
3----6.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.85→36.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5455 0 80 483 6018
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.552
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.572.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 814 10.1 %
Rwork0.253 7278 -
obs--62.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GCU.PARGCU.TOP
X-RAY DIFFRACTION3GOL.PARGOL.TOP
X-RAY DIFFRACTION4WATER_REP.PARAM
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.351
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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