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- PDB-7p43: Structure of CgGBE in complex with maltotriose -

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Basic information

Entry
Database: PDB / ID: 7p43
TitleStructure of CgGBE in complex with maltotriose
Components1,4-alpha-glucan-branching enzyme
KeywordsCARBOHYDRATE / glycogen branching enzyme
Function / homology
Function and homology information


cation binding / 1,4-alpha-glucan branching enzyme / : / 1,4-alpha-glucan branching enzyme activity / starch metabolic process / fungal biofilm matrix / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds / cytosol
Similarity search - Function
1,4-alpha-glucan-branching enzyme / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Immunoglobulin E-set ...1,4-alpha-glucan-branching enzyme / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta 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-maltotriose / 1,4-alpha-glucan-branching enzyme
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsBallut, L. / Conchou, L. / Violot, S. / Galisson, F. / Aghajari, N.
CitationJournal: Glycobiology / Year: 2022
Title: The Candida glabrata glycogen branching enzyme structure reveals unique features of branching enzymes of the Saccharomycetaceae phylum.
Authors: Conchou, L. / Martin, J. / Goncalves, I.R. / Galisson, F. / Violot, S. / Guilliere, F. / Aghajari, N. / Ballut, L.
History
DepositionJul 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 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
Revision 1.2Jan 31, 2024Group: 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: 1,4-alpha-glucan-branching enzyme
B: 1,4-alpha-glucan-branching enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,2974
Polymers162,2882
Non-polymers1,0092
Water12,466692
1
A: 1,4-alpha-glucan-branching enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6482
Polymers81,1441
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 1,4-alpha-glucan-branching enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6482
Polymers81,1441
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.720, 210.700, 90.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 1,4-alpha-glucan-branching enzyme / Glycogen-branching enzyme


Mass: 81143.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (fungus)
Strain: ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65
Gene: GLC3, CAGL0M03377g / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express
References: UniProt: Q6FJV0, 1,4-alpha-glucan branching enzyme
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 292 K / Method: evaporation / pH: 5.6
Details: 0.1M trisodium citrate pH 5.6, 10% PEG 4000, 10% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.93→47.05 Å / Num. obs: 128265 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 0.99 / Rrim(I) all: 0.09 / Net I/σ(I): 13.38
Reflection shellResolution: 1.93→2.04 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.76 / Num. unique obs: 20066 / CC1/2: 0.86 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZY

4bzy


Resolution: 1.93→47.05 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2175 6404 5 %
Rwork0.192 121704 -
obs0.1932 128108 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 270.38 Å2 / Biso mean: 56.9376 Å2 / Biso min: 23.23 Å2
Refinement stepCycle: final / Resolution: 1.93→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10881 0 68 692 11641
Biso mean--93.84 48.22 -
Num. residues----1377
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.93-1.950.51951850.48863498368388
1.95-1.970.39862150.414740834298100
1.97-1.990.33032110.357439954206100
1.99-2.020.35972110.318940114222100
2.02-2.050.31292130.298340374250100
2.05-2.070.33632110.289140024213100
2.07-2.10.30792150.264240764291100
2.1-2.140.28852090.258239914200100
2.14-2.170.26662110.246940254236100
2.17-2.20.28052120.238340314243100
2.2-2.240.26592130.228140414254100
2.24-2.280.23552130.217740464259100
2.28-2.330.25422130.20440424255100
2.33-2.370.22512120.195640614273100
2.37-2.430.27352120.204540284240100
2.43-2.480.23142140.195640764290100
2.48-2.550.24142130.1940444257100
2.55-2.610.24862140.191140724286100
2.61-2.690.22842140.191140564270100
2.69-2.780.24342130.191440594272100
2.78-2.880.22892150.195940784293100
2.88-2.990.24072140.20340624276100
2.99-3.130.23392160.194641054321100
3.13-3.290.22382150.18740904305100
3.29-3.50.20452160.182940984314100
3.5-3.770.18092160.161941194335100
3.77-4.150.16972180.149141354353100
4.15-4.750.14732170.135241604377100
4.75-5.980.17512220.163742044426100
5.98-47.050.18462310.178143794610100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.13970.0321-0.16340.16120.1620.24350.0386-0.14610.19440.21970.00690.29940.0081-0.10930.00020.3429-0.00220.03070.29540.02560.3333-5.07318.23159.066
20.52970.3454-0.03671.0156-0.1667-0.0014-0.0150.0507-0.08240.04610.0066-0.1470.00550.004500.29860.0099-0.02810.2903-0.00140.230616.45217.34551.608
30.0642-0.00580.17580.24810.07680.19-0.13260.18910.0312-0.03840.0641-0.03470.0979-0.0052-00.28850.0008-0.02240.35440.06350.427221.5244.09339.248
40.48530.1849-0.11060.41160.16590.2425-0.05440.03160.30210.0430.0475-0.06140.03610.039200.2685-0.009-0.0210.28130.0260.404521.17150.77647.203
50.0885-0.03640.07260.0602-0.02980.14220.05370.11780.6403-0.10850.13410.0057-0.0405-0.096-0.00020.2668-0.00240.00730.2784-0.00320.632411.13166.20153.256
60.1364-0.1259-0.12630.1668-0.02350.26880.12720.0805-0.0659-0.0101-0.0236-0.10890.19180.014900.553-0.0201-0.03040.46240.02630.292536.3099.52219.66
70.28320.04230.05680.04690.0850.16820.15570.1090.1802-0.1506-0.0268-0.6430.0621-0.0531-00.54270.02680.15240.51870.05680.602356.36819.42210.983
80.45340.0458-0.02710.14980.16610.22230.1640.21240.7617-0.1558-0.01320.0132-0.0045-0.068-0.01250.50830.06640.09460.57830.25050.585532.28134.74910.575
90.5886-0.07380.21520.3876-0.18940.20730.17680.41390.2961-0.2073-0.14290.03220.0789-0.11790.08990.55310.1021-0.02020.76710.15760.186823.06122.1762.543
100.0948-0.0366-0.040.3594-0.00370.07590.34340.45780.797-0.2398-0.14080.26030.0467-0.06910.06870.60640.18490.01140.9810.50450.93786.66741.6052.722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 19:60 )A19 - 60
2X-RAY DIFFRACTION2( CHAIN A AND RESID 61:469 )A61 - 469
3X-RAY DIFFRACTION3( CHAIN A AND RESID 470:519 )A470 - 519
4X-RAY DIFFRACTION4( CHAIN A AND RESID 520:677 )A520 - 677
5X-RAY DIFFRACTION5( CHAIN A AND RESID 678:706 )A678 - 706
6X-RAY DIFFRACTION6( CHAIN B AND RESID 24:81 )B24 - 81
7X-RAY DIFFRACTION7( CHAIN B AND RESID 82:176 )B82 - 176
8X-RAY DIFFRACTION8( CHAIN B AND RESID 177:270 )B177 - 270
9X-RAY DIFFRACTION9( CHAIN B AND RESID 271:535 )B271 - 535
10X-RAY DIFFRACTION10( CHAIN B AND RESID 536:706 )B536 - 706

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