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- PDB-3pha: The crystal structure of the W169Y mutant of alpha-glucosidase (g... -

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Basic information

Entry
Database: PDB / ID: 3pha
TitleThe crystal structure of the W169Y mutant of alpha-glucosidase (gh31 family) from Ruminococcus obeum atcc 29174 in complex with acarbose
Componentsalpha-glucosidase
Keywordshydrolase/hydrolase inhibitor / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / STRUCTURALCOMPLEX / MCSG / MIDWEST CENTER FOR STRUCTURAL GENOMICS / HYDROLASE / (beta/alpha)8-barrel / hydrolase-hydrolase inhibitor complex
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
alpha-acarbose / Glycosyl hydrolase, family 31
Similarity search - Component
Biological speciesBlautia obeum ATCC 29174 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.173 Å
AuthorsTan, K. / Tesar, C. / 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 (gh31 family) from Ruminococcus obeum atcc 29174 in complex with acarbose
Authors: Tan, K. / Tesar, C. / Keigher, L. / Babnigg, G. / Joachimiak, A.
History
DepositionNov 3, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionNov 24, 2010ID: 3NXM
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 19, 2017Group: Advisory / Database references ...Advisory / Database references / Polymer sequence / Source and taxonomy / Structure summary
Category: entity / entity_poly ...entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _entity.formula_weight / _entity.pdbx_ec ..._entity.formula_weight / _entity.pdbx_ec / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / 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 / struct_conn
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_atom_id / _atom_site.label_comp_id / _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.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_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Sep 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alpha-glucosidase
B: alpha-glucosidase
C: alpha-glucosidase
D: alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,2888
Polymers309,7064
Non-polymers2,5824
Water10,827601
1
A: alpha-glucosidase
B: alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,1444
Polymers154,8532
Non-polymers1,2912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-44 kcal/mol
Surface area44330 Å2
MethodPISA
2
C: alpha-glucosidase
D: alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,1444
Polymers154,8532
Non-polymers1,2912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-40 kcal/mol
Surface area44240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.032, 125.955, 133.580
Angle α, β, γ (deg.)90.00, 107.72, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe chains A and B, C and D form dimers respectively.

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Components

#1: Protein
alpha-glucosidase /


Mass: 77426.430 Da / Num. of mol.: 4 / Mutation: W169Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blautia obeum ATCC 29174 (bacteria) / Gene: RUMOBE_03919 / Plasmid: PMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): PPK1037
References: UniProt: A5ZY13, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Polysaccharide
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-acarbose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M BIS-TRIS, 25% PEG3350, 10% ACARBOSE, 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: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 22, 2010 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.173→42.5 Å / Num. all: 143009 / Num. obs: 143009 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 14.4
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.4 / Num. unique all: 6648 / % possible all: 91.7

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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
Resolution: 2.173→42.415 Å / SU ML: 0.32 / σ(F): 0.09 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2653 6586 4.99 %random
Rwork0.1995 ---
all0.2029 131921 --
obs0.2029 131921 90.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.064 Å2 / ksol: 0.289 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.3062 Å20 Å2-2.6081 Å2
2--1.3975 Å2-0 Å2
3---9.9087 Å2
Refinement stepCycle: LAST / Resolution: 2.173→42.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21770 0 176 601 22547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822556
X-RAY DIFFRACTIONf_angle_d1.08630451
X-RAY DIFFRACTIONf_dihedral_angle_d18.9698477
X-RAY DIFFRACTIONf_chiral_restr0.0733031
X-RAY DIFFRACTIONf_plane_restr0.0043964
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.173-2.25060.37245200.30559656X-RAY DIFFRACTION70
2.2506-2.34070.34786000.275611372X-RAY DIFFRACTION82
2.3407-2.44730.33096390.253512047X-RAY DIFFRACTION87
2.4473-2.57630.33046110.250212425X-RAY DIFFRACTION90
2.5763-2.73760.34296740.250112778X-RAY DIFFRACTION92
2.7376-2.9490.28777040.229113118X-RAY DIFFRACTION95
2.949-3.24560.28497330.219313382X-RAY DIFFRACTION97
3.2456-3.71510.26226730.188813661X-RAY DIFFRACTION98
3.7151-4.67960.21277040.148413444X-RAY DIFFRACTION97
4.6796-42.42310.19917280.149113452X-RAY DIFFRACTION96
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.4637-0.16580.23960.14420.110.31770.06010.0923-0.1446-0.03510.04960.2835-0.0710.0209-0.08290.04010.0184-0.07840.0692-0.02960.48116.6519-1.639438.2881
21.34120.04190.29450.1263-0.01040.20330.00540.076-0.063-0.03560.0614-0.079-0.00830.1594-0.07110.0977-0.0221-0.0410.2109-0.09840.444645.18312.900649.4677
30.7768-0.1046-0.10780.29070.07140.0840.04060.0534-0.0097-0.15430.00010.0652-0.0460.009-0.03190.14210.00280.00690.0799-0.0240.0794-13.505-1.8537101.1852
40.91710.17520.25280.2970.24080.1330.00860.0158-0.2326-0.05420.0235-0.0446-0.05930.0503-0.03110.14790.00010.03240.07330.03620.128525.00252.4046112.6774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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