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- PDB-7u3a: Structure of the Streptomyces venezuelae GlgX-c-di-GMP complex -

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Basic information

Entry
Database: PDB / ID: 7u3a
TitleStructure of the Streptomyces venezuelae GlgX-c-di-GMP complex
ComponentsGlycogen debranching enzyme GlgX
KeywordsHYDROLASE / c-di-GMP / GlgX / glycogen / glycogen debranching enzyme / second messenger / development / 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-C2E / Glycogen debranching enzyme GlgX
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.34 Å
AuthorsSchumacher, M.A.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycogen debranching enzyme GlgX
B: Glycogen debranching enzyme GlgX
C: Glycogen debranching enzyme GlgX
D: Glycogen debranching enzyme GlgX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,4318
Polymers320,6694
Non-polymers2,7624
Water00
1
A: Glycogen debranching enzyme GlgX
B: Glycogen debranching enzyme GlgX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,7154
Polymers160,3342
Non-polymers1,3812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint2 kcal/mol
Surface area48260 Å2
MethodPISA
2
C: Glycogen debranching enzyme GlgX
D: Glycogen debranching enzyme GlgX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,7154
Polymers160,3342
Non-polymers1,3812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-2 kcal/mol
Surface area47580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.470, 127.660, 179.720
Angle α, β, γ (deg.)90.000, 93.730, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glycogen debranching enzyme GlgX


Mass: 80167.234 Da / Num. of mol.: 4
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-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.: 4 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 40% ethylene glycol, 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.34→89.67 Å / Num. obs: 42293 / % possible obs: 99.5 % / Redundancy: 2 % / CC1/2: 0.977 / Rpim(I) all: 0.095 / Rsym value: 0.102 / Net I/σ(I): 6.2
Reflection shellResolution: 3.34→3.42 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2854 / CC1/2: 0.891 / Rpim(I) all: 0.228 / Rsym value: 0.323

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7U39

7u39


Resolution: 3.34→89.67 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2748 2000 4.73 %
Rwork0.2052 40293 -
obs0.2085 42293 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.25 Å2 / Biso mean: 36.6654 Å2 / Biso min: 15.5 Å2
Refinement stepCycle: final / Resolution: 3.34→89.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22058 0 184 0 22242
Biso mean--45.05 --
Num. residues----2770
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 (%)
3.34-3.420.29871370.24952854299199
3.42-3.520.3381390.251828833022100
3.52-3.620.34311440.24442860300499
3.62-3.740.3051500.24372821297199
3.74-3.870.34071320.22912867299999
3.87-4.020.31921370.209228743011100
4.02-4.210.25761420.198728643006100
4.21-4.430.2261500.181328553005100
4.43-4.710.24091430.172429063049100
4.71-5.070.26231450.180728933038100
5.07-5.580.27151370.197828793016100
5.58-6.390.27421440.196229053049100
6.39-8.050.21761530.200528853038100
8.05-89.670.23651470.17812947309499
Refinement TLS params.Method: refined / Origin x: 61.7258 Å / Origin y: 17.1057 Å / Origin z: 44.749 Å
111213212223313233
T0.2172 Å2-0.0659 Å20.0152 Å2-0.1645 Å20.0215 Å2--0.2124 Å2
L0.232 °2-0.0042 °20.0477 °2-0.1891 °20.0764 °2--0.6853 °2
S-0.0134 Å °-0.0483 Å °-0.0046 Å °-0.0083 Å °-0.0362 Å °0.0063 Å °-0.0383 Å °0.0312 Å °0.0417 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 705
2X-RAY DIFFRACTION1allB1 - 705
3X-RAY DIFFRACTION1allC2 - 705
4X-RAY DIFFRACTION1allD2 - 705
5X-RAY DIFFRACTION1allR201
6X-RAY DIFFRACTION1allT201
7X-RAY DIFFRACTION1allU201
8X-RAY DIFFRACTION1allV201

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