[English] 日本語
Yorodumi
- PDB-5f7c: Crystal structure of Family 31 alpha-glucosidase (BT_0339) from B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f7c
TitleCrystal structure of Family 31 alpha-glucosidase (BT_0339) from Bacteroides thetaiotaomicron
ComponentsAlpha-glucosidase
KeywordsHYDROLASE / Family Glycoside Hydrolase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like 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 ...Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like 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
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsChaudet, M.M. / Rose, D.R.
CitationJournal: Biochem. Cell Biol. / Year: 2016
Title: Suggested alternative starch utilization system from the human gut bacterium Bacteroides thetaiotaomicron.
Authors: Chaudet, M.M. / Rose, D.R.
History
DepositionDec 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-glucosidase
B: Alpha-glucosidase
C: Alpha-glucosidase
D: Alpha-glucosidase


Theoretical massNumber of molelcules
Total (without water)353,8814
Polymers353,8814
Non-polymers00
Water1,20767
1
A: Alpha-glucosidase


Theoretical massNumber of molelcules
Total (without water)88,4701
Polymers88,4701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-glucosidase


Theoretical massNumber of molelcules
Total (without water)88,4701
Polymers88,4701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha-glucosidase


Theoretical massNumber of molelcules
Total (without water)88,4701
Polymers88,4701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alpha-glucosidase


Theoretical massNumber of molelcules
Total (without water)88,4701
Polymers88,4701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Alpha-glucosidase
C: Alpha-glucosidase


Theoretical massNumber of molelcules
Total (without water)176,9412
Polymers176,9412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-24 kcal/mol
Surface area45260 Å2
MethodPISA
6
B: Alpha-glucosidase
D: Alpha-glucosidase


Theoretical massNumber of molelcules
Total (without water)176,9412
Polymers176,9412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-19 kcal/mol
Surface area43820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.340, 75.000, 232.860
Angle α, β, γ (deg.)90.000, 95.140, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Alpha-glucosidase /


Mass: 88470.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_0339
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8AAX3, alpha-glucosidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M Ammonium Sulfate, 0.05 M Bis-Tris:HCl pH 6.5, 30% (v/v) Pentaerythritol Ethoxylate (15/4 EO/OH), 0.1 M Sodium formate pH 7.0, 12% w/v Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→48.81 Å / Num. obs: 87516 / % possible obs: 99.98 % / Redundancy: 7.6 % / Net I/σ(I): 6.67
Reflection shellResolution: 2.6→2.693 Å / % possible all: 99.87

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementResolution: 2.6→48.81 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.65 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3491 1999 2.28 %
Rwork0.3025 85512 -
obs0.3036 87511 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.41 Å2 / Biso mean: 59.5763 Å2 / Biso min: 16.25 Å2
Refinement stepCycle: final / Resolution: 2.6→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19929 0 0 67 19996
Biso mean---50.17 -
Num. residues----2491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00720517
X-RAY DIFFRACTIONf_angle_d1.04927877
X-RAY DIFFRACTIONf_chiral_restr0.0382916
X-RAY DIFFRACTIONf_plane_restr0.0053579
X-RAY DIFFRACTIONf_dihedral_angle_d15.357345
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5999-2.66490.37641410.361260576198
2.6649-2.7370.41411410.347760116152
2.737-2.81750.391420.352560746216
2.8175-2.90850.40731420.348560706212
2.9085-3.01240.37771430.344461096252
3.0124-3.1330.34321420.335560726214
3.133-3.27550.40451410.323461056246
3.2755-3.44820.4261430.319160626205
3.4482-3.66420.31271410.30360426183
3.6642-3.9470.38691450.29161816326
3.947-4.34390.30691420.263860876229
4.3439-4.9720.26161440.253361446288
4.972-6.26210.34261440.285861886332
6.2621-48.82340.34831480.307863106458

+
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