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- PDB-7ekw: Crystal Structure of the Candida Glabrata Glycogen Debranching En... -

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Basic information

Entry
Database: PDB / ID: 7ekw
TitleCrystal Structure of the Candida Glabrata Glycogen Debranching Enzyme (D535N) in complex with maltotetrose
Components4-alpha-glucanotransferase
KeywordsSUGAR BINDING PROTEIN / Glycogen Debranching Enzyme
Function / homology
Function and homology information


amylo-alpha-1,6-glucosidase / amylo-alpha-1,6-glucosidase activity / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / beta-maltose 4-alpha-glucanotransferase activity / glycogen biosynthetic process / glycogen catabolic process / cytoplasm
Similarity search - Function
Glycogen debranching enzyme, metazoa / Glycogen debranching enzyme / Eukaryotic glycogen debranching enzyme, N-terminal domain / Glycogen debranching enzyme, central domain / Glycogen debranching enzyme, glucanotransferase domain / N-terminal domain from the human glycogen debranching enzyme / Glycogen debranching enzyme, glucanotransferase domain / Central domain of human glycogen debranching enzyme / Glycogen debranching enzyme, C-terminal / Amylo-alpha-1,6-glucosidase ...Glycogen debranching enzyme, metazoa / Glycogen debranching enzyme / Eukaryotic glycogen debranching enzyme, N-terminal domain / Glycogen debranching enzyme, central domain / Glycogen debranching enzyme, glucanotransferase domain / N-terminal domain from the human glycogen debranching enzyme / Glycogen debranching enzyme, glucanotransferase domain / Central domain of human glycogen debranching enzyme / Glycogen debranching enzyme, C-terminal / Amylo-alpha-1,6-glucosidase / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Glycogen debranching enzyme
Similarity search - Component
Biological speciesCandida glabrata CBS 138 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsShen, M. / Xiang, S.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870769 China
National Natural Science Foundation of China (NSFC)32071205 China
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Crystal structures of glycogen-debranching enzyme mutants in complex with oligosaccharides.
Authors: Shen, M. / Gong, X. / Xiang, S.
History
DepositionApr 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: 4-alpha-glucanotransferase
B: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)351,4293
Polymers351,0872
Non-polymers3421
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint4 kcal/mol
Surface area120240 Å2
Unit cell
Length a, b, c (Å)160.250, 198.940, 134.590
Angle α, β, γ (deg.)90.000, 104.870, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 4-alpha-glucanotransferase / / Amylo-alpha-1 / 6-glucosidase / Dextrin 6-alpha-D-glucosidase / Glycogen debrancher / Glycogen ...Amylo-alpha-1 / 6-glucosidase / Dextrin 6-alpha-D-glucosidase / Glycogen debrancher / Glycogen debranching enzyme / Oligo-1 / 4-1 / 4-glucantransferase


Mass: 175543.547 Da / Num. of mol.: 2 / Mutation: D535N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata CBS 138 (fungus) / Strain: CBS 138 / Gene: GDB1, CAGL0G09977g / Production host: Escherichia coli (E. coli)
References: UniProt: Q6FSK0, 4-alpha-glucanotransferase, amylo-alpha-1,6-glucosidase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 5000 MME,0.1 M Tris pH7.0,5% Tasimate pH7.0, 3.5mM TCEP hydrochiloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97939 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 3.1→25.75 Å / Num. obs: 73585 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC1/2: 0.991 / Net I/σ(I): 6.7
Reflection shellResolution: 3.1→3.27 Å / Num. unique obs: 10713 / CC1/2: 0.564 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D0F

5d0f


Resolution: 3.1→25.26 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2718 3764 5.13 %
Rwork0.248 69640 -
obs0.2493 73404 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 217.62 Å2 / Biso mean: 101.9921 Å2 / Biso min: 41.16 Å2
Refinement stepCycle: final / Resolution: 3.1→25.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24507 0 23 0 24530
Biso mean--116.11 --
Num. residues----3046
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.140.39311430.389225712714100
3.14-3.180.41821330.384825572690100
3.18-3.220.37111490.371425712720100
3.22-3.270.36541220.368526162738100
3.27-3.320.37121350.351425512686100
3.32-3.370.3521330.331425842717100
3.37-3.430.36161450.334625372682100
3.43-3.480.30851170.323426182735100
3.48-3.550.33971330.315626272760100
3.55-3.620.31531380.303225372675100
3.62-3.690.3261330.288125812714100
3.69-3.770.29211380.285225902728100
3.77-3.860.30561340.278725922726100
3.86-3.950.29491140.261625812695100
3.95-4.060.26131430.265125842727100
4.06-4.180.24921550.241725362691100
4.18-4.310.23851600.237425682728100
4.31-4.470.26031310.229525862717100
4.47-4.640.2721490.221125922741100
4.64-4.850.25291320.226625882720100
4.85-5.110.26811490.212925822731100
5.11-5.420.26221310.214625792710100
5.42-5.840.25971670.230925782745100
5.84-6.420.26361390.23642584272399
6.42-7.330.23071500.22232542269299
7.33-9.150.22611560.18072576273299
9.16-25.260.19231350.17322632276799
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)
12.347-0.4958-0.15023.0653-0.29621.45620.1101-0.4401-0.44550.00910.1160.5250.412-0.6592-0.02950.7268-0.2537-0.06750.95370.02310.8391-56.6464.63745.119
22.1515-1.1174-0.36313.4080.79012.6720.3562-0.03080.743-0.2540.0742-0.5351-0.11930.663-0.30560.64550.07860.15830.9055-0.11590.9753-100.11610.57341.858
32.5981-0.46820.25481.7922-0.11151.09380.1098-0.0602-0.8967-0.1181-0.0279-0.04620.7431-0.05890.01250.8779-0.0695-0.04250.5233-0.09870.7271-33.37-10.3139.688
43.2319-1.22790.08372.6480.17350.97820.26970.22791.009-0.2213-0.1083-0.6175-0.38640.1239-0.06830.71110.08160.25910.5806-0.00440.8134-123.38726.23438.487
52.77031.70580.5441.5606-0.79792.0292-0.22510.7979-0.097-1.43780.1418-0.18220.24590.08120.14032.2246-0.00720.06410.8329-0.42310.9474-47.573-15.542-0.22
61.1371-0.064-1.60560.20750.75482.46650.10930.7904-0.1728-0.4208-0.07580.191-0.4181-0.43620.27771.63970.27740.30171.49550.22231.4353-112.75832.538-2.552
74.33041.08960.83582.84190.38761.7569-0.0217-0.2284-0.0687-0.0977-0.047-0.33580.36610.12150.08850.69120.1-0.00410.64930.00870.8544-10.6253.84343.484
82.91420.5777-0.92283.5309-0.47311.73660.0467-0.2081-0.2928-0.0408-0.09510.12370.0179-0.0331-0.0060.69260.2320.13080.68860.01680.7344-146.11412.41842.825
92.7801-0.02850.33.3626-0.9032.4148-0.2518-0.38580.38440.7904-0.0194-0.8219-0.2827-0.28960.1270.63240.0398-0.23320.6386-0.19520.5565-36.97631.71856.599
104.0106-0.33010.43212.7691-0.46793.22920.44040.3298-0.8599-0.03880.02640.4347-0.0084-0.621-0.32940.50740.1921-0.09470.6014-0.01110.5877-120.361-16.89451.497
112.9317-0.11220.69464.22690.17073.1782-0.2318-0.06530.818-0.22870.07161.7148-0.5998-1.1348-0.17290.3480.4782-0.16410.873-0.32190.956-68.99349.33647.397
124.3423-0.4669-0.06942.4914-0.60362.63340.6230.9826-1.7316-0.4205-0.4631-0.09450.41370.02580.22130.56410.3765-0.19120.6044-0.6871.0969-89.527-34.69238.915
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:131 )A3 - 131
2X-RAY DIFFRACTION2( CHAIN B AND RESID 3:131 )B3 - 131
3X-RAY DIFFRACTION3( CHAIN A AND ( RESID 132:237 OR RESID 499:749 ) )A132 - 237
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 132:237 OR RESID 499:749 ) )A499 - 749
5X-RAY DIFFRACTION4( CHAIN B AND ( RESID 132:237 OR RESID 499:749 ) )B132 - 237
6X-RAY DIFFRACTION4( CHAIN B AND ( RESID 132:237 OR RESID 499:749 ) )B499 - 749
7X-RAY DIFFRACTION5( CHAIN A AND RESID 238:498 )A238 - 498
8X-RAY DIFFRACTION6( CHAIN B AND RESID 238:498 )B238 - 498
9X-RAY DIFFRACTION7( CHAIN A AND RESID 750:869 )A750 - 869
10X-RAY DIFFRACTION8( CHAIN B AND RESID 750:869 )B750 - 869
11X-RAY DIFFRACTION9( CHAIN A AND RESID 870:1022 )A870 - 1022
12X-RAY DIFFRACTION10( CHAIN B AND RESID 870:1022 )B870 - 1022
13X-RAY DIFFRACTION11( CHAIN A AND RESID 1023:1528 )A1023 - 1528
14X-RAY DIFFRACTION12( CHAIN B AND RESID 1023:1528 )B1023 - 1528

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