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

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Basic information

Entry
Database: PDB / ID: 7ejt
TitleCrystal Structure of the Candida Glabrata Glycogen Debranching Enzyme (W470A) in complex with maltoheptaose
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: 3.2 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 2, 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)354,0488
Polymers350,8592
Non-polymers3,1896
Water0
1
A: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,1054
Polymers175,4291
Non-polymers1,6753
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint5 kcal/mol
Surface area58440 Å2
MethodPISA
2
B: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,9434
Polymers175,4291
Non-polymers1,5133
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area58250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.387, 199.268, 133.743
Angle α, β, γ (deg.)90.000, 100.770, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 1528 or resid 2004 or resid 2002))
21(chain B and (resid 3 through 1528 or resid 2004 or resid 2002))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 1528 or resid 2004 or resid 2002))A3 - 1528
121(chain A and (resid 3 through 1528 or resid 2004 or resid 2002))A2004
131(chain A and (resid 3 through 1528 or resid 2004 or resid 2002))A2002
211(chain B and (resid 3 through 1528 or resid 2004 or resid 2002))B3 - 1528
221(chain B and (resid 3 through 1528 or resid 2004 or resid 2002))B2004
231(chain B and (resid 3 through 1528 or resid 2004 or resid 2002))B2002

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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: 175429.406 Da / Num. of mol.: 2 / Mutation: W470A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata CBS 138 (fungus) / Strain: CBS 138 / Gene: GDB1 / 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.: 3 / 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
#3: 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
#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.: 2 / 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
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: 2.94 Å3/Da / Density % sol: 58.1 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
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: 0.97908 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 3.2→40.48 Å / Num. obs: 66972 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 13.43
Reflection shellResolution: 3.2→3.26 Å / Num. unique obs: 3348 / CC1/2: 0.624

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D0F

5d0f


Resolution: 3.2→40.48 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2675 3360 5.09 %
Rwork0.2549 62711 -
obs0.2556 66071 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 223.74 Å2 / Biso mean: 113.0356 Å2 / Biso min: 59.88 Å2
Refinement stepCycle: final / Resolution: 3.2→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24538 0 215 0 24753
Biso mean--126.74 --
Num. residues----3052
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A14608X-RAY DIFFRACTION10.084TORSIONAL
12B14608X-RAY DIFFRACTION10.084TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.250.40621550.416125992754100
3.25-3.290.3761460.38225602706100
3.29-3.350.3741300.381226382768100
3.35-3.40.39551430.373226062749100
3.4-3.460.38691310.363225892720100
3.46-3.520.42511240.361326552779100
3.52-3.590.36421360.335825892725100
3.59-3.660.40621290.352726032732100
3.66-3.740.37331320.336126242756100
3.74-3.830.28611490.310326142763100
3.83-3.930.34251490.3372583273299
3.93-4.030.33741230.291426162739100
4.03-4.150.2871580.274525852743100
4.15-4.280.25631470.26425792726100
4.28-4.440.25551430.254626232766100
4.44-4.610.24431410.245726232764100
4.61-4.820.2341310.231525942725100
4.82-5.080.24541440.222726342778100
5.08-5.390.2261320.219926272759100
5.4-5.810.26321470.234726252772100
5.81-6.390.24481260.236126342760100
6.39-7.310.2841470.235326182765100
7.31-9.190.20171520.184826322784100
9.2-40.480.17291450.16952661280699
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)
12.7760.7106-0.68072.55630.32412.54430.0413-0.24940.05360.03410.13530.29850.2051-0.4828-0.37980.6231-0.0456-0.00461.07890.11380.6304-52.6401-4.008549.0255
21.27340.9315-0.09491.47771.08721.94870.0839-0.1634-0.35120.41750.0622-0.38880.82490.2167-0.68171.18060.2015-0.0750.89150.0380.9941-27.5026-30.501442.8979
31.542-0.66441.43931.9925-1.67094.21960.1115-0.1356-0.2167-0.18360.22340.04170.3462-0.1213-0.27281.0709-0.0490.00690.8166-0.09410.8523-45.5771-23.25122.5491
42.1886-0.13750.30921.7412-0.00360.45710.0720.0486-0.0865-0.00350.0261-0.01130.35630.1016-0.02540.78250.0335-0.04220.95270.00780.5378-30.3177-13.138541.6268
53.09980.76890.7243.2641.36511.4604-0.0603-0.41030.13730.2235-0.0799-0.07190.19370.07650.30770.58180.1599-0.09361.2347-0.03670.4848-6.863-3.720344.1922
61.6147-0.93070.48062.53390.03862.2741-0.1373-0.21240.40570.34020.1216-0.2150.0205-0.08530.18260.6022-0.0242-0.07541.0827-0.15090.6765-32.959823.527759.2456
72.3954-1.1604-0.41873.46070.72872.99330.0603-0.060.211-0.49870.06710.7037-0.5558-0.3865-0.16210.77660.1442-0.16220.8780.01650.9066-69.038338.625746.2287
81.2820.38470.15312.9102-0.65062.41810.0815-0.13090.1759-0.00640.2359-0.35990.00270.3516-0.09560.6860.11180.04650.7437-0.22320.8545-93.2524.257536.2867
91.72521.33490.41240.486-0.17391.49610.2061-0.09240.17980.011-0.07830.1867-0.7723-0.2356-0.13251.24470.2940.0750.636-0.20450.9882-118.178631.596336.0428
101.00090.4052-1.17740.89681.89665.8018-0.18070.55730.1222-0.1273-0.20860.3342-0.5339-0.72830.05441.20170.2420.00980.96010.03470.9924-109.976424.0765-7.2253
112.3716-0.3405-0.43920.1791.3810.0226-0.09010.344-0.08340.0014-0.0839-0.4101-0.29410.12220.74910.18050.02410.6003-0.10830.6379-116.28514.164334.0847
121.91170.3013-0.14891.6932-1.19442.3009-0.0244-0.18960.0425-0.02650.1139-0.0015-0.3238-0.3182-0.17140.76020.24950.05891.0586-0.19320.6514-138.90695.437641.7172
132.6649-0.24150.11072.77470.332.5634-0.2491-0.2773-0.58490.50320.13790.47640.1635-0.0898-0.14310.8280.15130.12570.56140.08740.76-111.2102-22.640950.5039
143.1676-0.1294-0.54093.56770.32972.1187-0.419-0.2949-1.17070.01320.3118-0.62120.58780.28170.00411.08850.31570.03940.6352-0.10731.4528-81.4963-40.361136.2777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 131 )A3 - 131
2X-RAY DIFFRACTION2chain 'A' and (resid 132 through 237 )A132 - 237
3X-RAY DIFFRACTION3chain 'A' and (resid 238 through 498 )A238 - 498
4X-RAY DIFFRACTION4chain 'A' and (resid 499 through 749 )A499 - 749
5X-RAY DIFFRACTION5chain 'A' and (resid 750 through 869 )A750 - 869
6X-RAY DIFFRACTION6chain 'A' and (resid 870 through 1022 )A870 - 1022
7X-RAY DIFFRACTION7chain 'A' and (resid 1203 through 1528 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 131 )B3 - 131
9X-RAY DIFFRACTION9chain 'B' and (resid 132 through 237 )B132 - 237
10X-RAY DIFFRACTION10chain 'B' and (resid 238 through 498 )B238 - 498
11X-RAY DIFFRACTION11chain 'B' and (resid 499 through 749 )B499 - 749
12X-RAY DIFFRACTION12chain 'B' and (resid 750 through 869 )B750 - 869
13X-RAY DIFFRACTION13chain 'B' and (resid 870 through 1022 )B870 - 1022
14X-RAY DIFFRACTION14chain 'B' and (resid 1023 through 1528 )B0

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