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

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Basic information

Entry
Database: PDB / ID: 7eku
TitleCrystal Structure of the Candida Glabrata Glycogen Debranching Enzyme (W958A)
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 species[Candida] 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: To Be Published
Title: Crystal Structure of the Candida Glabrata Glycogen Debranching Enzyme (W958A)
Authors: Shen, M. / Xiang, S.
History
DepositionApr 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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


Theoretical massNumber of molelcules
Total (without water)350,8592
Polymers350,8592
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-1 kcal/mol
Surface area120100 Å2
Unit cell
Length a, b, c (Å)160.221, 200.651, 259.976
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 283 or resid 288...
21(chain B and resid 3 through 1527)

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAVALVAL(chain A and (resid 3 through 283 or resid 288...AA3 - 2833 - 283
12VALVALGLYGLY(chain A and (resid 3 through 283 or resid 288...AA288 - 304288 - 304
13ALAALAGLUGLU(chain A and (resid 3 through 283 or resid 288...AA3 - 15273 - 1527
14ASNASNLYSLYS(chain A and (resid 3 through 283 or resid 288...AA337 - 341337 - 341
15SERSERHISHIS(chain A and (resid 3 through 283 or resid 288...AA344 - 384344 - 384
16TYRTYRASPASP(chain A and (resid 3 through 283 or resid 288...AA388 - 432388 - 432
17ILEILEGLUGLU(chain A and (resid 3 through 283 or resid 288...AA441 - 1527441 - 1527
21ALAALAGLUGLU(chain B and resid 3 through 1527)BB3 - 15273 - 1527

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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: W958A
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

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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 Å3/Da / Density % sol: 58.94 %
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: Apr 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→46.8 Å / Num. obs: 75998 / % possible obs: 99.9 % / Redundancy: 7.402 % / Biso Wilson estimate: 84.39 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.107 / Χ2: 0.913 / Net I/σ(I): 15.39 / Num. measured all: 562556 / Scaling rejects: 70
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.1-3.187.5550.951.9542072556955690.7321.02100
3.18-3.277.550.7312.5840833540954080.8210.784100
3.27-3.367.5550.5463.4539956528952890.90.586100
3.36-3.477.5490.3874.8138992516551650.9450.416100
3.47-3.587.5360.2996.2337448496949690.9660.321100
3.58-3.717.5380.2218.3136046478247820.9830.237100
3.71-3.857.5070.17910.3434990466146610.9880.193100
3.85-47.4750.13713.3133729451345120.9920.147100
4-4.187.4410.10716.6131961429542950.9950.115100
4.18-4.387.4230.08919.3930538411541140.9970.096100
4.38-4.627.3810.07722.5229038393439340.9970.083100
4.62-4.97.3360.0724.0627259371637160.9970.075100
4.9-5.247.2850.06625.7225424349034900.9980.071100
5.24-5.667.2690.06625.3323864328432830.9970.071100
5.66-6.27.1360.06326.2621644303330330.9980.068100
6.2-6.937.0690.05529.3419256272527240.9980.059100
6.93-87.2780.04533.6317832245024500.9990.049100
8-9.87.1410.03838.5414690205720570.9990.041100
9.8-13.866.970.03440.3611396163516350.9990.037100
13.86-46.86.1270.03636.5755889629120.9970.03994.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5d06

5d06


Resolution: 3.1→46.8 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2731 2713 3.57 %
Rwork0.2311 73222 -
obs0.2326 75935 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.08 Å2 / Biso mean: 86.5856 Å2 / Biso min: 31.62 Å2
Refinement stepCycle: final / Resolution: 3.1→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24309 0 0 0 24309
Num. residues----3023
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A13639X-RAY DIFFRACTION11.878TORSIONAL
12B13639X-RAY DIFFRACTION11.878TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.160.45071440.422137943938100
3.16-3.220.38451240.369438663990100
3.22-3.280.35761360.309938093945100
3.28-3.350.3291630.288737883951100
3.35-3.430.31351370.276238123949100
3.43-3.520.35171390.278538193958100
3.52-3.610.33361420.284538403982100
3.61-3.720.3091440.287238533997100
3.72-3.840.28851430.265438013944100
3.84-3.980.29521430.237438413984100
3.98-4.140.28751470.223938513998100
4.14-4.320.26931390.217238553994100
4.32-4.550.24461420.213338483990100
4.55-4.840.2631430.199638513994100
4.84-5.210.24211410.193638604001100
5.21-5.730.25891480.215238824030100
5.73-6.560.26971430.227138904033100
6.56-8.260.24481450.21439304075100
8.26-46.80.20671500.1764032418299
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)
10.0089-0.0099-0.010.0130.00620.03910.1130.03770.15560.00070.1022-0.04870.02380.06850.00020.3961-0.09050.14490.4088-0.04130.543638.2003104.6975173.373
20.0710.0094-0.02940.0592-0.02270.04750.1958-0.0625-0.0017-0.1027-0.09720.03880.08430.290600.43010.0647-0.04040.4786-0.03490.278178.4161100.211216.6086
30.2176-0.1271-0.18260.33610.16880.26490.2078-0.04280.34-0.01940.0061-0.1668-0.31840.0530.90310.45590.02090.3190.17280.15340.444814.6298119.154168.6024
40.21330.00170.11720.07240.07120.14190.1751-0.0467-0.1113-0.0409-0.0150.01870.28570.05780.00010.5821-0.0096-0.130.38430.03670.348655.95183.5907219.1079
50.2624-0.05410.07040.27080.09280.38160.22960.16030.20220.00070.2220.3323-0.301-0.29980.77410.65570.07280.25010.64820.28380.594626.6123123.4825127.3707
60.4005-0.1218-0.18760.5071-0.1530.52250.0142-0.3177-0.05230.34880.1573-0.0458-0.0056-0.00260.80770.86740.0201-0.11550.47140.24330.168369.379874.9748258.5042
70.1213-0.0229-0.07690.0348-0.00010.05390.07930.0412-0.00510.0312-0.15120.0488-0.2098-0.0453-00.43640.07950.13050.50630.03870.5001-7.6901105.0447173.8517
80.15970.01190.06020.0267-0.01760.03640.1672-0.1134-0.0322-0.0169-0.10080.18540.0368-0.15360.00010.4548-0.1383-0.01260.55320.08580.486532.696496.6862215.5328
90.15720.10810.12180.15450.05060.1345-0.2621-0.0507-0.13330.09720.13260.22920.08580.02-0.05130.38750.03790.1550.40630.05550.332219.453977.5574185.8176
100.07950.00240.00630.05240.01790.06390.1241-0.00960.20060.0333-0.01660.16980.0085-0.0482-00.36380.02180.10440.3437-0.00790.452157.3927127.1134207.6521
110.0739-0.0860.04990.38380.07750.3021-0.27680.0096-0.34340.00310.1383-0.33090.13690.2925-0.22870.28080.09080.26250.455-0.01540.57251.260.2131175.5428
120.33770.03190.02170.1683-0.04020.07860.2012-0.29380.7640.1461-0.0838-0.0962-0.24160.12930.16570.4251-0.15470.10910.485-0.37150.662587.2675145.5086221.1043
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 3:131))A3 - 131
2X-RAY DIFFRACTION2chain 'B' and ((resseq 3:131))B3 - 131
3X-RAY DIFFRACTION3chain 'A' and ((resseq 132:237) or (resseq 499:749))A0
4X-RAY DIFFRACTION4chain 'B' and ((resseq 132:237) or (resseq 499:749))B0
5X-RAY DIFFRACTION5chain 'A' and ((resseq 238:498))A238 - 498
6X-RAY DIFFRACTION6chain 'B' and ((resseq 238:498))B238 - 498
7X-RAY DIFFRACTION7chain 'A' and ((resseq 750:869))A750 - 869
8X-RAY DIFFRACTION8chain 'B' and ((resseq 750:869))B750 - 869
9X-RAY DIFFRACTION9chain 'A' and ((resseq 870:1022))A0
10X-RAY DIFFRACTION10chain 'B' and ((resseq 870:1022))B0
11X-RAY DIFFRACTION11chain 'A' and ((resseq 1023:1527))A0
12X-RAY DIFFRACTION12chain 'B' and ((resseq 1023:1528))B0

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