[English] 日本語
Yorodumi
- PDB-8b81: The structure of Gan1D W433A in complex with cellobiose-6-phosphate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b81
TitleThe structure of Gan1D W433A in complex with cellobiose-6-phosphate
ComponentsPutative 6-phospho-beta-galactobiosidase
KeywordsHYDROLASE / glycoside hydrolase / GH1 / cellobiose-6-phosphate / 6-phospho-beta-glucosidase
Function / homology
Function and homology information


6-phospho-beta-galactosidase / 6-phospho-beta-galactosidase activity / carbohydrate catabolic process / beta-glucosidase activity / cytosol
Similarity search - Function
Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-cellobiose-6-phosphate / IMIDAZOLE / Putative 6-phospho-beta-galactobiosidase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.585 Å
AuthorsSnyder, J. / Lansky, S. / Zehavi, A. / Shoham, Y. / Shoham, G.
Funding support Israel, 1items
OrganizationGrant numberCountry
Not funded Israel
CitationJournal: To Be Published
Title: The structure of Gan1D W433A in complex with cellobiose-6-phosphate
Authors: Snyder, J. / Lansky, S. / Zehavi, A. / Shoham, Y. / Shoham, G.
History
DepositionOct 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative 6-phospho-beta-galactobiosidase
B: Putative 6-phospho-beta-galactobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4268
Polymers110,3052
Non-polymers1,1216
Water17,835990
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-2 kcal/mol
Surface area31500 Å2
Unit cell
Length a, b, c (Å)107.900, 68.380, 149.800
Angle α, β, γ (deg.)90.000, 99.360, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-635-

HOH

-
Components

#1: Protein Putative 6-phospho-beta-galactobiosidase


Mass: 55152.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: gan1D / Production host: Escherichia coli (E. coli) / References: UniProt: W8QF82, 6-phospho-beta-galactosidase
#2: Polysaccharide 6-O-phosphono-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 422.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose-6-phosphate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1b_1-5_6*OPO/3O/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+0)][P]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 990 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 19% polyethylene glycol 8K, 3% MPD, 0.1 M imidazole buffer pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.585→50 Å / Num. obs: 141155 / % possible obs: 96.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 8.7
Reflection shellResolution: 1.585→1.68 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 1.82 / Num. unique obs: 20970 / % possible all: 89.2

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8B80

8b80


Resolution: 1.585→49.269 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2013 2816 2 %
Rwork0.1691 138146 -
obs0.1697 140962 96.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.02 Å2 / Biso mean: 27.5809 Å2 / Biso min: 10.93 Å2
Refinement stepCycle: final / Resolution: 1.585→49.269 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7730 0 74 990 8794
Biso mean--35.8 36.97 -
Num. residues----948
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5855-1.61280.37071030.3707503671
1.6128-1.64210.33341410.299688797
1.6421-1.67370.28831400.2614688897
1.6737-1.70790.26381420.238691097
1.7079-1.7450.27441400.2226689798
1.745-1.78560.29441410.2084695898
1.7856-1.83030.2411410.1994698798
1.8303-1.87980.22751420.1998693598
1.8798-1.93510.23921430.1948700498
1.9351-1.99750.23161420.185695998
1.9975-2.06890.20421400.1778691897
2.0689-2.15180.18641430.1729698498
2.1518-2.24970.20411430.1699702599
2.2497-2.36830.22471440.1725701998
2.3683-2.51670.18931430.1636704699
2.5167-2.7110.19111450.1626708099
2.711-2.98380.17131450.1645711399
2.9838-3.41540.22171440.1713706498
3.4154-4.30270.191450.145713599
4.3027-49.2690.14881490.1338730199

+
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