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- PDB-7u39: Structure of the apo form of Streptomyces venezuelae GlgX, the gl... -

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Basic information

Entry
Database: PDB / ID: 7u39
TitleStructure of the apo form of Streptomyces venezuelae GlgX, the glycogen debranching enzyme
ComponentsGlycogen debranching enzyme GlgX
KeywordsHYDROLASE / GlgX / glycogen debranching enzyme / glycogen / Streptomyces / c-di-GMP / development / apo form
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
Glycogen debranching enzyme GlgX
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.51 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
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
K: Glycogen debranching enzyme GlgX
L: Glycogen debranching enzyme GlgX


Theoretical massNumber of molelcules
Total (without water)962,00712
Polymers962,00712
Non-polymers00
Water9,332518
1
A: Glycogen debranching enzyme GlgX
E: Glycogen debranching enzyme GlgX


Theoretical massNumber of molelcules
Total (without water)160,3342
Polymers160,3342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-7 kcal/mol
Surface area49940 Å2
MethodPISA
2
B: Glycogen debranching enzyme GlgX
D: Glycogen debranching enzyme GlgX


Theoretical massNumber of molelcules
Total (without water)160,3342
Polymers160,3342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-6 kcal/mol
Surface area50690 Å2
MethodPISA
3
C: Glycogen debranching enzyme GlgX
I: Glycogen debranching enzyme GlgX


Theoretical massNumber of molelcules
Total (without water)160,3342
Polymers160,3342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-8 kcal/mol
Surface area50350 Å2
MethodPISA
4
F: Glycogen debranching enzyme GlgX
H: Glycogen debranching enzyme GlgX


Theoretical massNumber of molelcules
Total (without water)160,3342
Polymers160,3342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-8 kcal/mol
Surface area50350 Å2
MethodPISA
5
G: Glycogen debranching enzyme GlgX
L: Glycogen debranching enzyme GlgX


Theoretical massNumber of molelcules
Total (without water)160,3342
Polymers160,3342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-6 kcal/mol
Surface area50040 Å2
MethodPISA
6
J: Glycogen debranching enzyme GlgX
K: Glycogen debranching enzyme GlgX


Theoretical massNumber of molelcules
Total (without water)160,3342
Polymers160,3342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-8 kcal/mol
Surface area49840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.496, 204.856, 195.719
Angle α, β, γ (deg.)90.000, 90.430, 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.: 12
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O

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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: 3.78 Å3/Da / Density % sol: 67.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 9% propanol, 675 mM ammonium citrate/ammonium hydroxide pH 8.5

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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: Mar 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.51→67.92 Å / Num. obs: 131795 / % possible obs: 83.5 % / Redundancy: 1.7 % / CC1/2: 0.969 / Rpim(I) all: 0.0116 / Rsym value: 0.165 / Net I/σ(I): 5.5
Reflection shellResolution: 3.51→3.55 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4072 / CC1/2: 0.802 / Rpim(I) all: 0.363 / Rsym value: 0.438

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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: 2VUY

2vuy


Resolution: 3.51→67.92 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2756 1920 1.46 %
Rwork0.2114 129875 -
obs0.2164 131795 83.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.92 Å2 / Biso mean: 48.238 Å2 / Biso min: 24.86 Å2
Refinement stepCycle: final / Resolution: 3.51→67.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms66806 0 0 518 67324
Biso mean---32.25 -
Num. residues----8409
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 (%)
3.66-3.750.366550.25014072412737
3.75-3.850.3188660.24194900496644
3.85-3.960.31411000.2325730583052
3.96-4.090.31181010.22157000710163
4.09-4.240.27581410.21048878901980
4.24-4.410.26731500.1978108591100998
4.41-4.610.25511640.1925110361120099
4.61-4.850.25231640.1866109721113699
4.85-5.150.24441700.1896110591122999
5.15-5.550.25371610.2061109991116099
5.55-6.110.30181640.2115110501121499
6.11-6.990.26521590.2169110711123099
6.99-8.810.27851620.2096110701123299
8.81-67.920.25321630.1956111791134299
Refinement TLS params.Method: refined / Origin x: 48.3097 Å / Origin y: 50.8553 Å / Origin z: 43.2698 Å
111213212223313233
T0.3498 Å2-0.0367 Å2-0.0028 Å2-0.294 Å20.0024 Å2--0.2456 Å2
L0.0975 °2-0.0086 °2-0.0039 °2-0.0384 °20.0059 °2--0.073 °2
S0.0145 Å °-0.0103 Å °0.0136 Å °-0.0195 Å °-0.0047 Å °-0.0029 Å °-0.0514 Å °0.0074 Å °-0.0109 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 705
2X-RAY DIFFRACTION1allB1 - 705
3X-RAY DIFFRACTION1allC1 - 705
4X-RAY DIFFRACTION1allD2 - 705
5X-RAY DIFFRACTION1allE1 - 705
6X-RAY DIFFRACTION1allF2 - 705
7X-RAY DIFFRACTION1allG2 - 705
8X-RAY DIFFRACTION1allH1 - 705
9X-RAY DIFFRACTION1allI2 - 705
10X-RAY DIFFRACTION1allJ1 - 705
11X-RAY DIFFRACTION1allK2 - 705
12X-RAY DIFFRACTION1allL2 - 705
13X-RAY DIFFRACTION1allN1 - 518

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