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- PDB-1k9d: The 1.7 A crystal structure of alpha-D-glucuronidase, a family-67... -

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Basic information

Entry
Database: PDB / ID: 1k9d
TitleThe 1.7 A crystal structure of alpha-D-glucuronidase, a family-67 glycoside hydrolase from Bacillus stearothermophilus T-1
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
Xylan alpha-1,2-glucuronidase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: 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)79,77614
Polymers78,5791
Non-polymers1,19713
Water11,710650
1
A: alpha-D-glucuronidase
hetero molecules

A: alpha-D-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,55328
Polymers157,1582
Non-polymers2,39426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)73.570, 73.570, 329.960
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: 78579.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: T1 / 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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 650 / 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: 2.84 Å3/Da / Density % sol: 56.69 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.00933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 3, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00933 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 94808 / Redundancy: 4 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 10.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3 % / Rmerge(I) obs: 0.382 / Num. unique all: 3008 / % possible all: 60.7
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 50 Å / % possible obs: 93.5 % / Num. measured all: 271828
Reflection shell
*PLUS
% possible obs: 60.7 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: initial and partial model based on 2.4A resolution data (unpublished)

Resolution: 1.7→35.9 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 274221.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.203 9105 10 %RANDOM
Rwork0.176 ---
obs0.176 91195 93.5 %-
all-94808 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.864 Å2 / ksol: 0.366973 e/Å3
Displacement parametersBiso mean: 20.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2--1.09 Å20 Å2
3----2.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.7→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5453 0 78 650 6181
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_d
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.682
X-RAY DIFFRACTIONc_scbond_it1.692
X-RAY DIFFRACTIONc_scangle_it2.492.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 1037 10 %
Rwork0.247 9316 -
obs--62.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3GOL.PARGOL.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.351
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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