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

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Basic information

Entry
Database: PDB / ID: 7ejp
TitleCrystal Structure of the Candida Glabrata Glycogen Debranching Enzyme (W470A) in complex with maltohexaose
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 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)354,2108
Polymers350,8592
Non-polymers3,3516
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint43 kcal/mol
Surface area117870 Å2
Unit cell
Length a, b, c (Å)156.537, 199.828, 133.878
Angle α, β, γ (deg.)90.000, 100.780, 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 2003))
21(chain B and (resid 3 through 1528 or resid 2003))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 1528 or resid 2003))A3 - 1528
121(chain A and (resid 3 through 1528 or resid 2003))A2003
211(chain B and (resid 3 through 1528 or resid 2003))B3 - 1528
221(chain B and (resid 3 through 1528 or resid 2003))B2003

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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, 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.: 2
Source method: isolated from a genetically manipulated source
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.: 2 / 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
[][D-1-deoxy-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: isolated from a genetically manipulated source
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: 2.95 Å3/Da / Density % sol: 58.3 %
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: 0.91769 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: 0.91769 Å / Relative weight: 1
ReflectionResolution: 3.1→38.44 Å / Num. obs: 73954 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.74
Reflection shellResolution: 3.1→3.15 Å / Num. unique obs: 3680 / CC1/2: 0.427

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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: 3.1→38.44 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 3798 5.21 %
Rwork0.2359 69119 -
obs0.2369 72917 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 212.86 Å2 / Biso mean: 110.2177 Å2 / Biso min: 49.89 Å2
Refinement stepCycle: final / Resolution: 3.1→38.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24538 0 224 0 24762
Biso mean--131.13 --
Num. residues----3052
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A14609X-RAY DIFFRACTION8.994TORSIONAL
12B14609X-RAY DIFFRACTION8.994TORSIONAL
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 (%)
3.1-3.140.35921300.39672509263999
3.14-3.180.38041540.385225612715100
3.18-3.220.41821230.36325202643100
3.22-3.270.38421530.368225692722100
3.27-3.320.35991410.334325262667100
3.32-3.370.35221380.341825652703100
3.37-3.430.34741290.319225792708100
3.43-3.480.35361580.313325302688100
3.48-3.550.32121320.31325912723100
3.55-3.620.3261380.291225602698100
3.62-3.690.32861470.289425282675100
3.69-3.770.31581270.282525862713100
3.77-3.860.30371410.266325692710100
3.86-3.950.28611410.273725512692100
3.95-4.060.30031320.25225622694100
4.06-4.180.24311420.236725572699100
4.18-4.320.24491600.236225442704100
4.32-4.470.22841370.226225652702100
4.47-4.650.27731420.220925692711100
4.65-4.860.22391400.213125652705100
4.86-5.110.25421440.203425692713100
5.11-5.430.22161340.207525662700100
5.43-5.850.24221460.218925552701100
5.85-6.440.25541430.2225752718100
6.44-7.370.26051540.216825642718100
7.37-9.260.1691310.175226042735100
9.26-38.440.1761410.16552580272198
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)
11.56480.42510.05012.1686-0.22792.12160.1812-0.08380.2570.01360.2147-0.4799-0.12280.4965-0.38710.57330.08570.00380.7429-0.2210.7657-15.1165-3.400336.3913
21.70390.53510.20581.1204-0.0871.70290.2309-0.05860.493-0.1531-0.13840.04-1.0791-0.2339-0.13571.17870.30120.04490.6431-0.12291.0401-40.036823.939636.2177
30.79160.61680.21870.86051.29024.4549-0.15540.33240.2584-0.1663-0.00690.3584-0.7589-0.52090.18521.2560.2030.0261.07820.06081.0764-31.87616.6275-7.1708
41.7854-0.0023-0.44551.15790.17231.14140.0894-0.03440.4117-0.0802-0.0087-0.1426-0.4423-0.2478-0.05680.67360.1971-0.00640.5845-0.09230.6215-38.15536.519734.2505
52.22950.0354-0.26671.5902-0.6471.7439-0.0458-0.35140.12370.06590.06510.097-0.3571-0.5361-0.06530.57310.24280.01140.9366-0.1760.554-60.7813-2.219841.8261
62.305-0.1369-0.12422.01380.63261.7761-0.2677-0.4832-0.49540.48520.11810.45540.2577-0.25750.13010.76130.16950.08310.63380.09160.7176-33.1031-30.348150.6272
73.31060.1932-0.24633.84280.07231.7552-0.25710.0197-1.1768-0.16180.29-0.70740.65880.294-0.00560.99470.30330.03460.676-0.28231.2863-1.4804-46.286829.5185
81.74140.1268-0.34512.58030.12522.12620.044-0.2299-0.08930.04160.01790.3120.2133-0.3165-0.11220.5509-0.0345-0.04481.12810.07370.579325.5762-11.476549.0062
91.65720.4521-0.09651.3121-0.42031.08390.1334-0.2748-0.39210.3233-0.0176-0.0710.80390.0914-0.13831.0570.189-0.09481.05170.02870.86550.6816-38.075442.9685
100.9537-0.29260.87921.53-1.44753.23880.0383-0.0345-0.1276-0.16950.1402-0.0490.3154-0.0236-0.14060.9085-0.0276-0.03140.9788-0.1090.800432.5844-30.95322.5281
111.5316-0.20170.14251.47370.09860.24830.0254-0.0821-0.04910.04720.1002-0.03030.3460.1966-0.09180.660.0531-0.06911.0355-0.00670.488947.8946-20.694541.6678
122.88670.87040.06331.88980.94271.2128-0.017-0.40790.13610.14880.0053-0.26540.20860.40150.04250.61840.1788-0.10521.3526-0.0640.515171.3502-11.325444.2867
131.8986-0.69720.39162.21220.38022.5012-0.2293-0.37520.43250.23550.1863-0.3401-0.10920.24910.01940.4869-0.0063-0.05561.051-0.13750.542245.305916.000459.2021
142.1-0.69810.1512.89460.21181.9892-0.162-0.38940.6523-0.12930.07030.6254-0.5755-0.39830.10330.82360.206-0.12791.0908-0.15781.027912.654232.916252.3621
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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