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- PDB-7u3b: Structure of S. venezuelae GlgX bound to c-di-GMP and acarbose (p... -

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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 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
Revision 1.3Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms ...pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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
Has protein modificationN

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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: 2.91 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

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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

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Phasing

PhasingMethod: molecular replacement

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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

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