[English] 日本語
Yorodumi
- PDB-5ay9: Crystal structure of Ruminococcus albus 4-O-beta-D-mannosyl-D-glu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ay9
TitleCrystal structure of Ruminococcus albus 4-O-beta-D-mannosyl-D-glucose phosphorylase (RaMP1)
Components4-O-beta-D-mannosyl-D-glucose phosphorylase
KeywordsTRANSFERASE / Glycoside hydrolase family 130
Function / homology
Function and homology information


4-O-beta-D-mannosyl-D-glucose phosphorylase / hexosyltransferase activity / cell wall organization / carbohydrate metabolic process
Similarity search - Function
4-O-beta-D-mannosyl-D-glucose phosphorylase / Mannoside phosphorylase / beta-1,4-mannooligosaccharide phosphorylase / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
4-O-beta-D-mannosyl-D-glucose phosphorylase
Similarity search - Component
Biological speciesRuminococcus albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsYe, Y. / Saburi, W. / Kato, K. / Yao, M.
CitationJournal: Febs Lett. / Year: 2016
Title: Structural insights into the difference in substrate recognition of two mannoside phosphorylases from two GH130 subfamilies
Authors: Ye, Y. / Saburi, W. / Odaka, R. / Kato, K. / Sakurai, N. / Komoda, K. / Nishimoto, M. / Kitaoka, M. / Mori, H. / Yao, M.
History
DepositionAug 11, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 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: 4-O-beta-D-mannosyl-D-glucose phosphorylase


Theoretical massNumber of molelcules
Total (without water)43,7001
Polymers43,7001
Non-polymers00
Water00
1
A: 4-O-beta-D-mannosyl-D-glucose phosphorylase

A: 4-O-beta-D-mannosyl-D-glucose phosphorylase

A: 4-O-beta-D-mannosyl-D-glucose phosphorylase


Theoretical massNumber of molelcules
Total (without water)131,1003
Polymers131,1003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area14150 Å2
ΔGint-63 kcal/mol
Surface area41880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.900, 88.900, 286.857
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein 4-O-beta-D-mannosyl-D-glucose phosphorylase / Mannosylglucose phosphorylase / RaMP1


Mass: 43700.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus albus (strain ATCC 27210 / DSM 20455 / JCM 14654 / NCDO 2250 / 7) (bacteria)
Strain: ATCC 27210 / DSM 20455 / JCM 14654 / NCDO 2250 / 7 / Gene: Rumal_0852 / Production host: Escherichia coli (E. coli)
References: UniProt: E6UIS7, 4-O-beta-D-mannosyl-D-glucose phosphorylase

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium nitrate, 0.1M Bis-Tris propane buffer, 20%(w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→46.01 Å / Num. obs: 15552 / % possible obs: 99.3 % / Redundancy: 9.1 % / Net I/σ(I): 14.7

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
Cootmodel building
RefinementResolution: 2.5→46.003 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2806 776 5 %
Rwork0.2389 --
obs0.2409 15516 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→46.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3059 0 0 0 3059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053126
X-RAY DIFFRACTIONf_angle_d1.0524242
X-RAY DIFFRACTIONf_dihedral_angle_d17.0851140
X-RAY DIFFRACTIONf_chiral_restr0.044464
X-RAY DIFFRACTIONf_plane_restr0.004556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.65660.38291280.33582415X-RAY DIFFRACTION100
2.6566-2.86170.36021290.30262452X-RAY DIFFRACTION100
2.8617-3.14970.36111270.292404X-RAY DIFFRACTION100
3.1497-3.60530.31371280.24862452X-RAY DIFFRACTION100
3.6053-4.54160.24311300.21722464X-RAY DIFFRACTION100
4.5416-46.0110.22881340.19922553X-RAY DIFFRACTION99

+
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://pdbjlvh1.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