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

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Basic information

Entry
Database: PDB / ID: 7ekx
TitleCrystal Structure of the Candida Glabrata Glycogen Debranching Enzyme (W470A E564Q) in complex with maltononaose
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 catabolic process / glycogen biosynthetic 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: 3.4 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)353,6856
Polymers350,8572
Non-polymers2,8284
Water00
1
A: 4-alpha-glucanotransferase
hetero molecules

hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,1044
Polymers175,4281
Non-polymers1,6753
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x+1/2,y+1/2,z1
Buried area2780 Å2
ΔGint22 kcal/mol
Surface area58640 Å2
MethodPISA
2
B: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,0863
Polymers175,4281
Non-polymers1,6572
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint24 kcal/mol
Surface area57700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.654, 206.280, 258.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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: 175428.406 Da / Num. of mol.: 2 / Mutation: W470A, E564Q
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-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1 / Source method: obtained synthetically
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: 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
#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,7,6/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][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: 3.07 Å3/Da / Density % sol: 59.88 %
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: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.4→46.16 Å / Num. obs: 58913 / % possible obs: 99.6 % / Redundancy: 7.3 % / CC1/2: 0.998 / Net I/σ(I): 8.31
Reflection shellResolution: 3.4→3.49 Å / Num. unique obs: 4334 / CC1/2: 0.588

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5d0f

5d0f


Resolution: 3.4→46.15 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3034 2929 4.97 %
Rwork0.2723 55953 -
obs0.2739 58882 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 304.3 Å2 / Biso mean: 141.0566 Å2 / Biso min: 67.78 Å2
Refinement stepCycle: final / Resolution: 3.4→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24538 0 191 0 24729
Biso mean--145.46 --
Num. residues----3052
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.460.47351250.43826482773100
3.46-3.520.47291350.414326482783100
3.52-3.580.39731290.406326442773100
3.58-3.650.40031500.380726432793100
3.65-3.720.45971390.364926462785100
3.72-3.80.36261440.341126432787100
3.8-3.890.38881560.337826102766100
3.89-3.990.37631440.325126562800100
3.99-4.10.33481420.31426392781100
4.1-4.220.3811420.298526652807100
4.22-4.350.32931490.296726252774100
4.35-4.510.32571470.2952631277899
4.51-4.690.31871350.279726612796100
4.69-4.90.32211270.282626612788100
4.9-5.160.3121350.269926782813100
5.16-5.480.3461250.268226842809100
5.48-5.910.30111380.281826902828100
5.91-6.50.31721330.263726792812100
6.5-7.440.30511500.25742679282999
7.44-9.360.22441330.203627562889100
9.36-46.150.18251510.17812767291898
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)
11.3270.1299-1.19821.74570.16021.60370.2424-0.2451-0.1479-0.31640.090.3160.23680.149-0.27170.65450.0068-0.13751.45060.11630.876142.175-5.27142.811
23.0624-0.43360.25272.89890.78233.76980.3712-0.14610.348-0.0358-0.0363-0.1738-0.12290.6476-0.29170.6833-0.19860.10781.4909-0.20410.7691-1.8050.05942.954
31.3237-0.15510.19561.7580.26560.63250.044-0.039-0.41760.0627-0.05390.06640.3580.1815-0.04230.67350.0701-0.07951.25790.21790.792365.901-19.7638.231
43.08950.1486-0.61121.86780.3881.55490.50480.050.88770.0732-0.10460.3242-0.8717-0.0015-0.37780.97170.04550.35111.2935-0.1421.1557-24.45816.62940.671
50.74410.52441.07892.8132-1.10383.4597-0.11750.3002-0.3119-0.05420.2172-0.26490.3290.24970.00651.03590.032-0.0611.5252-0.05521.13954.261-23.49-2.846
62.41162.70690.51892.94990.85062.3406-0.58951.61750.7004-2.67070.35940.5401-0.71890.00220.14452.5426-0.02720.36351.72620.15191.3034-12.34625.2970.684
72.3094-0.46990.54521.97960.53392.78670.0324-0.06370.08330.1262-0.0611-0.36740.30180.43370.18290.6663-0.0275-0.05441.51390.12320.950588.22-5.47343.47
84.00250.2759-1.33522.631-1.12392.28880.32110.08950.83490.12420.30160.5357-0.3568-0.479-0.49070.71970.0270.03681.27290.13831.0196-47.6663.33944.183
93.2796-2.27760.16311.7704-0.75092.0732-0.224-0.00730.85290.25850.2193-0.5709-0.0960.69710.13820.7257-0.081-0.10281.571-0.06621.001860.90221.99355.546
101.6709-1.4181-0.56392.73380.54823.1930.28290.008-0.77760.01350.18060.62780.1099-0.6372-0.40060.5983-0.1782-0.20541.3389-0.17260.8992-22.763-27.0651.87
112.0638-0.2363-0.25482.70420.41682.0437-0.08260.18550.7834-0.01340.07470.2748-0.51650.01130.01750.82680.1125-0.0921.39070.10331.350329.4539.36744.898
124.00390.41070.02923.2408-0.0911.97890.22260.4372-0.8509-0.6160.0333-0.43650.73640.1644-0.14870.94870.229-0.15141.0009-0.33380.94326.941-45.50238.491
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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