[English] 日本語
Yorodumi
- PDB-7u3b: Structure of S. venezuelae GlgX bound to c-di-GMP and acarbose (p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7u3b
TitleStructure of S. venezuelae GlgX bound to c-di-GMP and acarbose (pH 8.5)
ComponentsGlycogen debranching enzyme GlgX
KeywordsHYDROLASE / GlgX / glycogen / acarbose / c-di-GMP / Streptomyces
Function / homology
Function and homology information


glycogen debranching enzyme activity / glycogen catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / nucleotide binding
Similarity search - Function
Glycogen debranching enzyme, GlgX type / Glycogen debranching enzyme GlgX/isoamylase, N-terminal Early set domain / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-A16 / Chem-C2E / PHOSPHATE ION / Glycogen debranching enzyme GlgX
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.6 Å
AuthorsSchumacher, M.A. / Tschowri, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130290 United States
CitationJournal: Nat Commun / Year: 2022
Title: Allosteric regulation of glycogen breakdown by the second messenger cyclic di-GMP.
Authors: Schumacher, M.A. / Wormann, M.E. / Henderson, M. / Salinas, R. / Latoscha, A. / Al-Bassam, M.M. / Singh, K.S. / Barclay, E. / Gunka, K. / Tschowri, N.
History
DepositionFeb 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Oct 18, 2023Group: 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
C: Glycogen debranching enzyme GlgX
D: Glycogen debranching enzyme GlgX
E: Glycogen debranching enzyme GlgX
F: Glycogen debranching enzyme GlgX
G: Glycogen debranching enzyme GlgX
H: Glycogen debranching enzyme GlgX
I: Glycogen debranching enzyme GlgX
J: Glycogen debranching enzyme GlgX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)651,12528
Polymers641,3388
Non-polymers9,78720
Water36020
1
C: Glycogen debranching enzyme GlgX
H: Glycogen debranching enzyme GlgX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,7817
Polymers160,3342
Non-polymers2,4475
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-3 kcal/mol
Surface area48600 Å2
MethodPISA
2
D: Glycogen debranching enzyme GlgX
F: Glycogen debranching enzyme GlgX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,8768
Polymers160,3342
Non-polymers2,5426
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-9 kcal/mol
Surface area48320 Å2
MethodPISA
3
E: Glycogen debranching enzyme GlgX
I: Glycogen debranching enzyme GlgX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,7817
Polymers160,3342
Non-polymers2,4475
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-3 kcal/mol
Surface area48260 Å2
MethodPISA
4
G: Glycogen debranching enzyme GlgX
J: Glycogen debranching enzyme GlgX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,6866
Polymers160,3342
Non-polymers2,3524
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint3 kcal/mol
Surface area47840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.839, 185.588, 184.671
Angle α, β, γ (deg.)90.000, 98.080, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Glycogen debranching enzyme GlgX


Mass: 80167.234 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Gene: glgX, DEJ46_08920 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5P2ALW6
#2: Chemical
ChemComp-A16 / 4-O-(4,6-dideoxy-4-{[(1S,2S,3S,4R,5S)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D-glucopyranosyl)-beta-D-glucopyranose


Mass: 485.480 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C19H35NO13 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.91 Å3/Da / Density % sol: 57.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 50% MPD, 0.1 M Tris pH 8.5 and 200 mM ammonium phosphate monobasic

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→48.5 Å / Num. obs: 83324 / % possible obs: 98.2 % / Redundancy: 1.7 % / CC1/2: 0.923 / Rpim(I) all: 0.17 / Rsym value: 0.199 / Net I/σ(I): 5.5
Reflection shellResolution: 3.6→3.78 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5752 / CC1/2: 0.667 / Rpim(I) all: 0.517 / Rsym value: 0.78

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7U3A

7u3a


Resolution: 3.6→48.5 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3075 2000 2.4 %
Rwork0.2366 81324 -
obs0.2383 83324 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 216.7 Å2 / Biso mean: 46.8686 Å2 / Biso min: 0.12 Å2
Refinement stepCycle: final / Resolution: 3.6→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44293 0 644 20 44957
Biso mean--70.45 15.05 -
Num. residues----5559
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6-3.690.39511410.28275752589398
3.69-3.790.32441440.2665833597799
3.79-3.90.33021420.25465777591999
3.9-4.030.331440.24915865600999
4.03-4.170.31711420.23265763590599
4.17-4.340.29671420.22435789593199
4.34-4.540.30011440.2215834597899
4.54-4.770.28241430.22175848599199
4.77-5.070.26141430.21685812595599
5.07-5.460.28781440.22995832597698
5.46-6.010.33691420.24875775591798
6.01-6.880.32791430.24655839598298
6.88-8.660.28961430.23985782592598
8.66-48.50.27061430.21075823596697

+
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://pdbjlc1.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