[English] 日本語
Yorodumi
- PDB-7p4c: Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p4c
TitleCrystal Structure of Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31, in complex with noncovalent Cyclophellitol Sulfamidate probe KK131
ComponentsOligosaccharide 4-alpha-D-glucosyltransferase
KeywordsHYDROLASE / glycoside hydrolase / GH31 / inhibitor / carbohydrate
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) / 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 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-5OV / OXALATE ION / Oligosaccharide 4-alpha-D-glucosyltransferase
Similarity search - Component
Biological speciesCellvibrio japonicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsWu, L. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council (ERC)AdG-322942 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: 1,6- epi-Cyclophellitol Cyclosulfamidate Is a Bona Fide Lysosomal alpha-Glucosidase Stabilizer for the Treatment of Pompe Disease.
Authors: Kok, K. / Kuo, C.L. / Katzy, R.E. / Lelieveld, L.T. / Wu, L. / Roig-Zamboni, V. / van der Marel, G.A. / Codee, J.D.C. / Sulzenbacher, G. / Davies, G.J. / Overkleeft, H.S. / Aerts, J.M.F.G. / Artola, M.
History
DepositionJul 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Oligosaccharide 4-alpha-D-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,04916
Polymers94,5931
Non-polymers1,45615
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer elutes as single peak
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-74 kcal/mol
Surface area28690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.000, 197.000, 102.156
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11AAA-1431-

HOH

-
Components

-
Protein , 1 types, 1 molecules AAA

#1: Protein Oligosaccharide 4-alpha-D-glucosyltransferase / Alpha-glucosidase 31B / CJAgd31B


Mass: 94592.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellvibrio japonicus (strain Ueda107) (bacteria)
Strain: Ueda107 / Gene: agd31B, CJA_3248 / Production host: Escherichia coli (E. coli)
References: UniProt: B3PEE6, oligosaccharide 4-alpha-D-glucosyltransferase

-
Non-polymers , 5 types, 446 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical ChemComp-5OV / (3aR,4S,5S,6R,7R,7aS)-7-(hydroxymethyl)-2,2-bis(oxidanylidene)-3a,4,5,6,7,7a-hexahydro-3H-benzo[d][1,2,3]oxathiazole-4,5,6-triol / Cyclophellitol Sulfamidate probe KK131


Mass: 255.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13NO7S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.8 M AMMONIUM SULFATE, 0.1 M HEPES (PH 7.0), 2% PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.86→102.31 Å / Num. obs: 97555 / % possible obs: 100 % / Redundancy: 24.6 % / Biso Wilson estimate: 35.281 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.025 / Rrim(I) all: 0.127 / Net I/σ(I): 14.5
Reflection shellResolution: 1.86→1.89 Å / Rmerge(I) obs: 2.839 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4790 / CC1/2: 0.618 / Rpim(I) all: 0.589 / Rrim(I) all: 2.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4b9y

4b9y


Resolution: 1.86→102.31 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.117
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.229 4828 4.949 %
Rwork0.1915 92720 -
all0.193 --
obs-97548 99.965 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.32 Å2
Baniso -1Baniso -2Baniso -3
1--1.361 Å2-0.68 Å20 Å2
2---1.361 Å20 Å2
3---4.415 Å2
Refinement stepCycle: LAST / Resolution: 1.86→102.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6237 0 83 431 6751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136519
X-RAY DIFFRACTIONr_bond_other_d0.0350.0175981
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.6478848
X-RAY DIFFRACTIONr_angle_other_deg2.3341.57913778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7175788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56222.145359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.814151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9291542
X-RAY DIFFRACTIONr_chiral_restr0.0780.2815
X-RAY DIFFRACTIONr_chiral_restr_other1.3370.21
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027418
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021574
X-RAY DIFFRACTIONr_nbd_refined0.1970.21173
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.25560
X-RAY DIFFRACTIONr_nbtor_refined0.1710.23031
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.22841
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2415
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.070.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1520.29
X-RAY DIFFRACTIONr_nbd_other0.2260.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.218
X-RAY DIFFRACTIONr_mcbond_it3.5164.1153143
X-RAY DIFFRACTIONr_mcbond_other3.5164.1143142
X-RAY DIFFRACTIONr_mcangle_it4.6366.1553934
X-RAY DIFFRACTIONr_mcangle_other4.6366.1563935
X-RAY DIFFRACTIONr_scbond_it4.2574.5293376
X-RAY DIFFRACTIONr_scbond_other4.1664.4933341
X-RAY DIFFRACTIONr_scangle_it6.366.6224914
X-RAY DIFFRACTIONr_scangle_other6.246.5644861
X-RAY DIFFRACTIONr_lrange_it7.70346.2817193
X-RAY DIFFRACTIONr_lrange_other7.70446.0727106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.9080.3663510.3566737X-RAY DIFFRACTION99.6625
1.908-1.9610.3353210.3356630X-RAY DIFFRACTION99.9712
1.961-2.0170.3013680.36371X-RAY DIFFRACTION99.9852
2.017-2.0790.2853460.2756224X-RAY DIFFRACTION100
2.079-2.1480.2883190.2546044X-RAY DIFFRACTION99.9686
2.148-2.2230.32940.2525879X-RAY DIFFRACTION100
2.223-2.3070.2652830.2275672X-RAY DIFFRACTION100
2.307-2.4010.2632990.2185448X-RAY DIFFRACTION100
2.401-2.5080.2462620.2055252X-RAY DIFFRACTION100
2.508-2.630.2782460.2115035X-RAY DIFFRACTION100
2.63-2.7720.2462500.2134799X-RAY DIFFRACTION100
2.772-2.9410.2862400.2114530X-RAY DIFFRACTION100
2.941-3.1440.2682240.2144265X-RAY DIFFRACTION100
3.144-3.3950.2162080.1924003X-RAY DIFFRACTION100
3.395-3.7190.1862010.1733679X-RAY DIFFRACTION100
3.719-4.1580.1881890.1483335X-RAY DIFFRACTION99.9716
4.158-4.8010.1581380.1313016X-RAY DIFFRACTION100
4.801-5.8790.1771270.1332557X-RAY DIFFRACTION100
5.879-8.3090.217930.1492041X-RAY DIFFRACTION100
8.309-102.310.201690.1711203X-RAY DIFFRACTION99.7647

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more