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- PDB-7xoi: Aspergillus sojae alpha-glucosidase AsojAgdL in complex with trehalose -

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Basic information

Entry
Database: PDB / ID: 7xoi
TitleAspergillus sojae alpha-glucosidase AsojAgdL in complex with trehalose
Components(alpha-glucosidase ...) x 2
KeywordsHYDROLASE / GH31 / alpha-glucosidase / transglucosylation
Function / homologyalpha-D-glucopyranose
Function and homology information
Biological speciesAspergillus sojae NBRC 4239 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTonozuka, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20K05956 Japan
CitationJournal: J.Struct.Biol. / Year: 2022
Title: Structural basis for proteolytic processing of Aspergillus sojae alpha-glucosidase L with strong transglucosylation activity.
Authors: Ding, Y. / Oyagi, A. / Miyasaka, Y. / Kozono, T. / Sasaki, N. / Kojima, Y. / Yoshida, M. / Matsumoto, Y. / Yasutake, N. / Nishikawa, A. / Tonozuka, T.
History
DepositionMay 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: alpha-glucosidase N-terminal polypeptide
B: alpha-glucosidase C-terminal polypeptide
C: alpha-glucosidase N-terminal polypeptide
D: alpha-glucosidase C-terminal polypeptide
E: alpha-glucosidase N-terminal polypeptide
F: alpha-glucosidase C-terminal polypeptide
G: alpha-glucosidase N-terminal polypeptide
H: alpha-glucosidase C-terminal polypeptide
I: alpha-glucosidase N-terminal polypeptide
J: alpha-glucosidase C-terminal polypeptide
K: alpha-glucosidase N-terminal polypeptide
L: alpha-glucosidase C-terminal polypeptide
M: alpha-glucosidase N-terminal polypeptide
N: alpha-glucosidase C-terminal polypeptide
O: alpha-glucosidase N-terminal polypeptide
P: alpha-glucosidase C-terminal polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)916,608121
Polymers888,80916
Non-polymers27,798105
Water35,5801975
1
A: alpha-glucosidase N-terminal polypeptide
B: alpha-glucosidase C-terminal polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,54815
Polymers111,1012
Non-polymers3,44713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20100 Å2
ΔGint-19 kcal/mol
Surface area30680 Å2
MethodPISA
2
C: alpha-glucosidase N-terminal polypeptide
D: alpha-glucosidase C-terminal polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,54815
Polymers111,1012
Non-polymers3,44713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20050 Å2
ΔGint-22 kcal/mol
Surface area30890 Å2
MethodPISA
3
E: alpha-glucosidase N-terminal polypeptide
F: alpha-glucosidase C-terminal polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,54815
Polymers111,1012
Non-polymers3,44713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20210 Å2
ΔGint-31 kcal/mol
Surface area30700 Å2
MethodPISA
4
G: alpha-glucosidase N-terminal polypeptide
H: alpha-glucosidase C-terminal polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,77016
Polymers111,1012
Non-polymers3,66814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20470 Å2
ΔGint-34 kcal/mol
Surface area30740 Å2
MethodPISA
5
I: alpha-glucosidase N-terminal polypeptide
J: alpha-glucosidase C-terminal polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,77016
Polymers111,1012
Non-polymers3,66814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20500 Å2
ΔGint-26 kcal/mol
Surface area30620 Å2
MethodPISA
6
K: alpha-glucosidase N-terminal polypeptide
L: alpha-glucosidase C-terminal polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,32714
Polymers111,1012
Non-polymers3,22612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19870 Å2
ΔGint-22 kcal/mol
Surface area30500 Å2
MethodPISA
7
M: alpha-glucosidase N-terminal polypeptide
N: alpha-glucosidase C-terminal polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,54815
Polymers111,1012
Non-polymers3,44713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20020 Å2
ΔGint-23 kcal/mol
Surface area30700 Å2
MethodPISA
8
O: alpha-glucosidase N-terminal polypeptide
P: alpha-glucosidase C-terminal polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,54815
Polymers111,1012
Non-polymers3,44713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20210 Å2
ΔGint-35 kcal/mol
Surface area30530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.325, 106.036, 206.366
Angle α, β, γ (deg.)90.58, 90.06, 92.20
Int Tables number1
Space group name H-MP1

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Components

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Alpha-glucosidase ... , 2 types, 16 molecules ACEGIKMOBDFHJLNP

#1: Protein
alpha-glucosidase N-terminal polypeptide


Mass: 61667.570 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus sojae NBRC 4239 (mold) / Strain: NBRC 4239 / Production host: Komagataella pastoris (fungus) / References: alpha-glucosidase
#2: Protein
alpha-glucosidase C-terminal polypeptide


Mass: 49433.605 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus sojae NBRC 4239 (mold) / Strain: NBRC 4239 / Production host: Komagataella pastoris (fungus) / References: alpha-glucosidase

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Sugars , 5 types, 97 molecules

#3: Polysaccharide
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 57
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 1983 molecules

#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1975 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Sequence details1. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) ...1. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. THE SEQUENCE INFORMATION IS AVAILABLE AT DDBJ WITH ACCESSION CODE DDBJ DM849390. 2. Residues -52 to 19 APVNTTTEDETAQIPAEAVIGYSDLEGDFDVAVLPFSNSTNNGLLFINTTIASIAAKEEGVSLEKREAEAEF is derived from the expression vector. Residues 20 to 30 QSKDGVEDLDG is derived from AsojAgdL. Residues 496 to 515 QGNATEKRSTAAVVKRQRSQ is proteolytically digested during the maturation. Residues 952 to 960 AVDHHHHHH 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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 13% polyethylene glycol 8000, 0.2 M ammonium acetate, 0.1 M sodium citrate buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→49.14 Å / Num. obs: 349142 / % possible obs: 97.3 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.088 / Net I/σ(I): 5.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 17217 / Rpim(I) all: 0.374 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W38

3w38


Resolution: 2.3→49.14 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.904 / Cross valid method: THROUGHOUT / ESU R: 0.445 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26685 16975 4.9 %RANDOM
Rwork0.2272 ---
obs0.22912 332166 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20.01 Å2
2--0.02 Å20.01 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.3→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms57152 0 1806 1978 60936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01360831
X-RAY DIFFRACTIONr_bond_other_d0.0350.01553178
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.69583286
X-RAY DIFFRACTIONr_angle_other_deg2.581.615122961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.01357192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1823.183296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.028158520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.19815280
X-RAY DIFFRACTIONr_chiral_restr0.0480.28036
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0269546
X-RAY DIFFRACTIONr_gen_planes_other0.0050.0214353
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1293.51628816
X-RAY DIFFRACTIONr_mcbond_other1.1293.51628815
X-RAY DIFFRACTIONr_mcangle_it1.8755.2735992
X-RAY DIFFRACTIONr_mcangle_other1.8755.2735993
X-RAY DIFFRACTIONr_scbond_it1.0813.6432015
X-RAY DIFFRACTIONr_scbond_other1.0813.6432016
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8485.4347295
X-RAY DIFFRACTIONr_long_range_B_refined3.28840.60667190
X-RAY DIFFRACTIONr_long_range_B_other3.26340.666934
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 1246 -
Rwork0.332 24396 -
obs--96.64 %

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