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- PDB-3nuk: THE CRYSTAL STRUCTURE OF THE W169Y mutant of ALPHA-GLUCOSIDASE (F... -

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Entry
Database: PDB / ID: 3nuk
TitleTHE CRYSTAL STRUCTURE OF THE W169Y mutant of ALPHA-GLUCOSIDASE (FAMILY 31) from RUMINOCOCCUS OBEUM ATCC 29174
ComponentsALPHA-GLUCOSIDASE
KeywordsHYDROLASE / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / (beta/alpha)8 barrel / glycosyle hydrolysis
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Immunoglobulin-like - #4040 / glycosyl hydrolase (family 31) / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain ...Immunoglobulin-like - #4040 / glycosyl hydrolase (family 31) / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Glycosyl hydrolase, family 31
Similarity search - Component
Biological speciesRuminococcus obeum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.055 Å
AuthorsTan, K. / Tesar, C. / Wilton, R. / Keigher, L. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: THE CRYSTAL STRUCTURE OF THE W169Y mutant of ALPHA-GLUCOSIDASE (FAMILY 31) from RUMINOCOCCUS OBEUM ATCC 29174
Authors: Tan, K. / Tesar, C. / Wilton, R. / Keigher, L. / Babnigg, G. / Joachimiak, A.
History
DepositionJul 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 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-GLUCOSIDASE
B: ALPHA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,9453
Polymers154,8532
Non-polymers921
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-17 kcal/mol
Surface area45270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.798, 125.531, 88.296
Angle α, β, γ (deg.)90.00, 107.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ALPHA-GLUCOSIDASE /


Mass: 77426.430 Da / Num. of mol.: 2 / Mutation: W169Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus obeum (bacteria) / Strain: ATCC 29174 / Gene: RUMOBE_03919 / Plasmid: PMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): PPK1037 / References: UniProt: A5ZY13
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M BIS-TRIS, 25% PEG3350, 10% Isomaltose, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.05→35 Å / Num. all: 87275 / Num. obs: 87275 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 19.8
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 98.1 % / Rmerge(I) obs: 0.704 / Mean I/σ(I) obs: 1.44 / % possible all: 98.1

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N04

3n04


Resolution: 2.055→34.696 Å / SU ML: 0.28 / σ(F): 0.11 / Phase error: 30.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 3862 5.04 %
Rwork0.1945 --
obs0.1972 76682 86.44 %
all-76682 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.204 Å2 / ksol: 0.273 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-21.0914 Å2-0 Å21.6543 Å2
2---10.8049 Å20 Å2
3----10.2865 Å2
Refinement stepCycle: LAST / Resolution: 2.055→34.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10770 0 6 326 11102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711085
X-RAY DIFFRACTIONf_angle_d1.02914944
X-RAY DIFFRACTIONf_dihedral_angle_d18.2934056
X-RAY DIFFRACTIONf_chiral_restr0.0731503
X-RAY DIFFRACTIONf_plane_restr0.0041955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0546-2.1280.36723020.3155992X-RAY DIFFRACTION71
2.128-2.21320.34163620.28226453X-RAY DIFFRACTION77
2.2132-2.31390.33553640.26216815X-RAY DIFFRACTION81
2.3139-2.43590.32763780.24286983X-RAY DIFFRACTION83
2.4359-2.58850.29263940.2197290X-RAY DIFFRACTION87
2.5885-2.78820.30113820.22147536X-RAY DIFFRACTION89
2.7882-3.06870.29664190.21017730X-RAY DIFFRACTION92
3.0687-3.51240.24383880.18448043X-RAY DIFFRACTION95
3.5124-4.42380.2034220.15927916X-RAY DIFFRACTION94
4.4238-34.70060.20344510.16788062X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2316-0.29520.10031.3176-0.40981.10410.0266-0.051-0.0095-0.05660.0071-0.0549-0.0362-0.0856-0.02540.2810.00740.02150.27840.00260.28250.423-2.547858.257
20.585-0.1182-0.3020.26910.0760.9148-0.0960.0734-0.0774-0.13350.0250.05070.0372-0.10070.0620.31910.017-0.00370.1623-0.01680.18771.22492.210217.4603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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