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- PDB-7u3d: Structure of S. venezuelae GlgX-c-di-GMP-acarbose complex (4.6) -

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Basic information

Entry
Database: PDB / ID: 7u3d
TitleStructure of S. venezuelae GlgX-c-di-GMP-acarbose complex (4.6)
ComponentsGlycogen debranching enzyme GlgX
KeywordsHYDROLASE / GlgX / glycogen / c-di-GMP / acarbose / Streptomyces development
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
alpha-acarbose / Chem-C2E / Glycogen debranching enzyme GlgX
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsSchumacher, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 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 27, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)326,01312
Polymers320,6694
Non-polymers5,3448
Water18,3031016
1
A: Glycogen debranching enzyme GlgX
F: Glycogen debranching enzyme GlgX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,0076
Polymers160,3342
Non-polymers2,6724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycogen debranching enzyme GlgX
C: Glycogen debranching enzyme GlgX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,0076
Polymers160,3342
Non-polymers2,6724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.881, 145.379, 229.466
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-1138-

HOH

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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: Polysaccharide
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp4Gc]{[(4+1)][<C2O2>]{}}}LINUCSPDB-CARE
#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.: 4 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1016 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 300, 100 mM NaCl and 0.1 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 PILATUS3 6M / Detector: PIXEL / Date: Feb 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→49.1 Å / Num. obs: 124127 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.995 / Rpim(I) all: 0.07 / Rsym value: 0.155 / Net I/σ(I): 11
Reflection shellResolution: 2.4→2.53 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8764 / CC1/2: 0.647 / Rpim(I) all: 0.0473 / Rsym value: 1.045

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7U3B

7u3b


Resolution: 2.4→47.41 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2347 1994 1.61 %
Rwork0.172 122133 -
obs0.1731 124127 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.69 Å2 / Biso mean: 39.7524 Å2 / Biso min: 19.19 Å2
Refinement stepCycle: final / Resolution: 2.4→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21795 0 360 1026 23181
Biso mean--42.71 38.96 -
Num. residues----2738
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 (%)
2.4-2.460.35991410.261786538794100
2.46-2.530.31321420.242486398781100
2.53-2.60.31821410.219986668807100
2.6-2.680.30181420.2186648806100
2.68-2.780.24751410.189186708811100
2.78-2.890.28211420.186286888830100
2.89-3.020.28491420.188186798821100
3.02-3.180.27941420.198287048846100
3.18-3.380.25091440.181287518895100
3.38-3.640.2451400.1768659879999
3.64-4.010.23181380.17748477861597
4.01-4.590.1611440.123488168960100
4.59-5.780.18791450.129688939038100
5.78-47.410.18971500.15391749324100
Refinement TLS params.Method: refined / Origin x: 14.4425 Å / Origin y: -37.319 Å / Origin z: 28.1626 Å
111213212223313233
T0.265 Å2-0.011 Å20.0062 Å2-0.2248 Å2-0.005 Å2--0.2439 Å2
L0.2413 °2-0.0103 °20.0505 °2-0.1507 °2-0.012 °2--0.2081 °2
S-0.0036 Å °0.0133 Å °-0.0324 Å °-0.0143 Å °-0 Å °-0.0068 Å °0.0378 Å °-0.0033 Å °0.0046 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 705
2X-RAY DIFFRACTION1allF1 - 706
3X-RAY DIFFRACTION1allQ1 - 201
4X-RAY DIFFRACTION1allB1 - 705
5X-RAY DIFFRACTION1allC1 - 706
6X-RAY DIFFRACTION1allT201
7X-RAY DIFFRACTION1allR201
8X-RAY DIFFRACTION1allG1
9X-RAY DIFFRACTION1allW201
10X-RAY DIFFRACTION1allE1
11X-RAY DIFFRACTION1allY1
12X-RAY DIFFRACTION1allS1 - 1059

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