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- PDB-4b9z: Crystal Structure of Agd31B, alpha-transglucosylase, complexed wi... -

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Basic information

Entry
Database: PDB / ID: 4b9z
TitleCrystal Structure of Agd31B, alpha-transglucosylase, complexed with Acarbose
ComponentsALPHA-GLUCOSIDASE, PUTATIVE, ADG31B
KeywordsHYDROLASE
Function / homology
Function and homology information


oligosaccharide 4-alpha-D-glucosyltransferase / oligosaccharide 4-alpha-D-glucosyltransferase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
: / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / glycosyl hydrolase (family 31) / 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 ...: / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / glycosyl hydrolase (family 31) / 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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-acarbose / OXALATE ION / DI(HYDROXYETHYL)ETHER / Oligosaccharide 4-alpha-D-glucosyltransferase
Similarity search - Component
Biological speciesCELLVIBRIO JAPONICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLarsbrink, J. / Izumi, A. / Hemsworth, G.R. / Davies, G.J. / Brumer, H.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Enzymology of Cellvibrio Japonicus Agd31B Reveals Alpha-Transglucosylase Activity in Glycoside Hydrolase Family 31
Authors: Larsbrink, J. / Izumi, A. / Hemsworth, G.R. / Davies, G.J. / Brumer, H.
History
DepositionSep 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_conn / struct_conn_type / struct_site / struct_site_gen
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 / _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 / _pdbx_database_status.status_code_sf / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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, PUTATIVE, ADG31B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,76324
Polymers92,5121
Non-polymers2,25123
Water7,999444
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)196.880, 196.880, 102.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein ALPHA-GLUCOSIDASE, PUTATIVE, ADG31B / / ALPHA-TRANSGLUCOSYLASE


Mass: 92511.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Plasmid: PENTR/SD/D-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3PEE6, alpha-glucosidase
#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.: 1
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
[][b-D-Gulp]{[(4+1)][b-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 466 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsK817 IS DERIVED FROM THE EXPRESSION VECTOR.

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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: 3.11 Å3/Da / Density % sol: 60.42 % / Description: NONE
Crystal growDetails: 1.8 M AMMONIUM SULFATE, 0.1 M HEPES (PH7.0), 2% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→51.38 Å / Num. obs: 79078 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 21.5 % / Biso Wilson estimate: 24.58 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 22.2
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 7.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B9Y

4b9y


Resolution: 2→49.734 Å / SU ML: 0.43 / σ(F): 1.91 / Phase error: 17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1874 3974 5 %
Rwork0.1607 --
obs0.162 79078 99.97 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.748 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.2253 Å20 Å20 Å2
2---3.2253 Å20 Å2
3---6.4505 Å2
Refinement stepCycle: LAST / Resolution: 2→49.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6203 0 142 444 6789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076545
X-RAY DIFFRACTIONf_angle_d1.0948853
X-RAY DIFFRACTIONf_dihedral_angle_d13.9092419
X-RAY DIFFRACTIONf_chiral_restr0.078935
X-RAY DIFFRACTIONf_plane_restr0.0051141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02440.2281170.1832651X-RAY DIFFRACTION100
2.0244-2.050.21611520.1762628X-RAY DIFFRACTION100
2.05-2.0770.20971360.16182645X-RAY DIFFRACTION100
2.077-2.10550.17451290.15582653X-RAY DIFFRACTION100
2.1055-2.13550.19131390.15752661X-RAY DIFFRACTION100
2.1355-2.16740.22971340.15712627X-RAY DIFFRACTION100
2.1674-2.20130.18441310.15822674X-RAY DIFFRACTION100
2.2013-2.23740.18621580.15562628X-RAY DIFFRACTION100
2.2374-2.27590.20991190.15292667X-RAY DIFFRACTION100
2.2759-2.31730.18361420.15952656X-RAY DIFFRACTION100
2.3173-2.36190.2191410.15812661X-RAY DIFFRACTION100
2.3619-2.41010.22671500.15972628X-RAY DIFFRACTION100
2.4101-2.46250.17631550.15842652X-RAY DIFFRACTION100
2.4625-2.51980.18961360.15982663X-RAY DIFFRACTION100
2.5198-2.58280.19731440.16172667X-RAY DIFFRACTION100
2.5828-2.65260.18081370.16392669X-RAY DIFFRACTION100
2.6526-2.73070.22191490.1682661X-RAY DIFFRACTION100
2.7307-2.81880.20881510.17782658X-RAY DIFFRACTION100
2.8188-2.91960.19831690.18152651X-RAY DIFFRACTION100
2.9196-3.03640.20841530.19092681X-RAY DIFFRACTION100
3.0364-3.17460.20891260.18462699X-RAY DIFFRACTION100
3.1746-3.34190.20181340.17732695X-RAY DIFFRACTION100
3.3419-3.55130.18351330.16232723X-RAY DIFFRACTION100
3.5513-3.82540.14521360.14442716X-RAY DIFFRACTION100
3.8254-4.21020.15551410.12582724X-RAY DIFFRACTION100
4.2102-4.81890.1361650.12632736X-RAY DIFFRACTION100
4.8189-6.06960.17581500.14732772X-RAY DIFFRACTION100
6.0696-49.74970.21851470.19312958X-RAY DIFFRACTION100
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)
10.81750.1392-0.03440.73130.65323.1528-0.11620.3716-0.1634-0.4718-0.05680.21030.088-0.53420.31570.44580.0252-0.08120.3948-0.19080.330164.141614.8218-2.6425
21.37670.44490.21741.40271.53282.6041-0.04220.3164-0.1103-0.5997-0.03880.0665-0.2398-0.12790.09420.49420.06570.02930.3055-0.13180.253875.767822.4403-3.092
30.2495-0.0680.02860.48310.01320.43510.02740.1016-0.0901-0.1404-0.03060.00130.11530.0186-0.01350.17620.01160.07820.1098-0.16640.196376.666318.584730.7409
40.685-0.3761-0.09141.042-0.08330.52360.00880.1295-0.0024-0.1877-0.0588-0.06380.0161-0.01930.03960.162-0.00020.05280.157-0.08910.181872.144945.288527.682
52.19630.5097-0.50162.3707-0.28141.28330.0415-0.02660.31210.1046-0.01590.2095-0.206-0.0919-0.03090.12890.0389-0.00210.1559-0.06370.246460.341358.751436.4046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 35:104)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 105:156)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 157:584)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 585:743)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 744:817)

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