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- PDB-5d06: Crystal Structure of the Candida Glabrata Glycogen Debranching Enzyme -

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Basic information

Entry
Database: PDB / ID: 5d06
TitleCrystal Structure of the Candida Glabrata Glycogen Debranching Enzyme
ComponentsUncharacterized protein
KeywordsSUGAR BINDING PROTEIN / TIM barrel / (alpha/alpha)6 barrel / hydrolase
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 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsZhai, L. / Xiang, S.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology2011CB910500 China
CitationJournal: Nat Commun / Year: 2016
Title: Crystal structure of glycogen debranching enzyme and insights into its catalysis and disease-causing mutations.
Authors: Zhai, L. / Feng, L. / Xia, L. / Yin, H. / Xiang, S.
History
DepositionAug 2, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)348,9472
Polymers348,9472
Non-polymers00
Water0
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)174,4731
Polymers174,4731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)174,4731
Polymers174,4731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.271, 198.950, 261.550
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
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA3 - 1528
211chain BB4 - 1528

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Components

#1: Protein Uncharacterized protein


Mass: 174473.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (fungus)
Strain: ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65
Gene: CAGL0G09977g / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta (DE3) / References: UniProt: Q6FSK0

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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: 58.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% PEG 5000 MME, 0.1 M Hepes pH 7.0, 5% tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.0391 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0391 Å / Relative weight: 1
ReflectionRedundancy: 6.9 % / Number: 379811 / Rsym value: 0.13 / D res high: 2.791 Å / D res low: 130.485 Å / Num. obs: 55270 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
10.9149.9910.0550.0556.9
7.7110.9110.0510.0517.4
6.37.7110.0790.0797
5.456.310.130.136.9
4.885.4510.1320.1327
4.454.8810.1360.1367
4.124.4510.1590.1596.9
3.864.1210.2170.2176.8
3.643.8610.3350.3356.7
3.453.6410.5220.5226.6
ReflectionResolution: 3.1→130.775 Å / Num. all: 73294 / Num. obs: 73294 / % possible obs: 97.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 79.5 Å2 / Rpim(I) all: 0.067 / Rrim(I) all: 0.128 / Rsym value: 0.109 / Net I/av σ(I): 4.965 / Net I/σ(I): 7.4 / Num. measured all: 242017
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.1-3.273.30.4821.535915108120.3050.5740.482299.3
3.27-3.473.30.2992.533757101860.1880.3550.2993.399.2
3.47-3.713.30.1833.93183395790.1130.2160.1835.198.9
3.71-43.30.1285.22954589310.0780.1510.1286.998.6
4-4.383.30.0966.42707581810.0580.1130.0969.198.3
4.38-4.93.30.0916.32428673600.0540.1060.09110.797.8
4.9-5.663.30.0936.12117864550.0550.1080.09311.297.1
5.66-6.933.20.0926.31687953320.0560.1080.09211.594.2
6.93-9.83.40.0687.71432542150.0410.080.06813.795.3
9.8-48.2173.20.0649.2722422430.0410.0760.06414.290.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
SCALA3.3.21data scaling
PDB_EXTRACT3.15data extraction
MOSFLM7.2.0data reduction
PHENIX1.9-1692phasing
RefinementMethod to determine structure: MAD / Resolution: 3.1→47.753 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2682 2606 3.56 %RANDOM
Rwork0.2336 70658 --
obs0.2349 73264 97.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 221.01 Å2 / Biso mean: 96.0727 Å2 / Biso min: 45.68 Å2
Refinement stepCycle: final / Resolution: 3.1→47.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24403 0 0 0 24403
Num. residues----3032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01325017
X-RAY DIFFRACTIONf_angle_d1.73733916
X-RAY DIFFRACTIONf_chiral_restr0.0773626
X-RAY DIFFRACTIONf_plane_restr0.0094403
X-RAY DIFFRACTIONf_dihedral_angle_d17.799272
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A13448X-RAY DIFFRACTION8.958TORSIONAL
12B13448X-RAY DIFFRACTION8.958TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.15640.35671340.34893745387999
3.1564-3.21710.41561230.33663748387199
3.2171-3.28270.38531380.3253762390099
3.2827-3.35410.34341560.30963767392399
3.3541-3.43210.34711400.29863721386199
3.4321-3.51790.30051370.27173730386799
3.5179-3.6130.31081400.26533763390399
3.613-3.71930.26261360.25553738387499
3.7193-3.83930.28351470.25183726387398
3.8393-3.97640.30071340.24523762389698
3.9764-4.13550.27011400.23273701384198
4.1355-4.32360.26571360.21613748388498
4.3236-4.55140.21431430.20723729387298
4.5514-4.83630.23381310.20253691382297
4.8363-5.20930.22321420.20513717385997
5.2093-5.73280.2671350.22293693382896
5.7328-6.56050.2791330.23343663379695
6.5605-8.25860.27251270.21763593372092
8.2586-47.75890.21331340.18763661379591
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)
11.746-0.65-0.282.76050.00451.510.1007-0.05310.7540.00830.0539-0.6839-0.47020.4704-0.14210.5541-0.14690.14260.59720.05621.482738.7248104.2368174.3755
22.540.0537-0.40912.2775-0.69273.06260.3164-0.0862-0.3667-0.141-0.0664-0.1340.53630.3066-0.20940.53290.0156-0.13620.4399-0.09351.156477.694698.1569218.6166
32.2945-0.4709-0.5241.03080.41491.20350.2850.15260.698-0.13-0.1434-0.2947-0.7668-0.0554-0.13840.85470.02460.21730.41850.13711.450615.264118.9624169.4768
41.73540.02040.13240.44080.25561.13330.26920.0051-0.67790.04350.13210.08210.639-0.1367-0.32970.7365-0.2152-0.33910.43340.09721.505154.384482.2984221.2884
50.5165-0.3934-1.07781.0511.26253.71090.23810.37430.3631-0.06-0.04180.2283-0.5863-0.514-0.17790.94670.12130.1890.86080.44621.526127.2132122.8642128.0556
61.1839-0.1360.55470.0790.33542.4863-0.1324-0.1777-0.28710.250.11540.26970.2319-0.12830.05231.4288-0.0894-0.27020.64350.22581.654368.974474.4866261.8301
72.7296-0.5682-0.39041.37450.31861.8210.12420.254-0.0572-0.085-0.26480.2576-0.351-0.49350.13270.48740.13530.12010.5318-0.04351.1759-7.2952104.948174.5093
81.6322-0.13690.08451.32030.04871.67190.1829-0.104-0.32830.0986-0.0420.18470.2172-0.5384-0.13920.4131-0.291-0.12310.70130.22181.240831.994695.8912217.7774
91.8527-0.6446-0.17512.23820.04621.6131-0.2694-0.2224-0.2440.51190.15530.50070.22050.00110.08930.47260.03670.20410.36920.12951.046319.625777.3879187.4495
101.66030.4519-0.45421.3169-0.59192.57250.53760.07110.44090.10660.07460.2596-0.5577-0.6221-0.56220.4790.03360.29630.36880.06551.134357.0912125.5012209.3197
112.2494-0.2755-0.17482.6055-0.1322.4938-0.17840.0188-0.52790.02860.0632-0.82350.61920.66950.09750.52380.20340.15530.63920.07221.406951.341259.544177.3467
122.09110.2365-0.04721.6265-0.64222.16220.5346-0.69820.62010.6979-0.2243-0.101-0.87610.3073-0.15221.0068-0.60180.48320.1528-0.42731.486287.65143.5634222.3464
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 4:131))B4 - 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 1023:1528))A0
12X-RAY DIFFRACTION12chain 'B' and ((resseq 1023:1528))B0

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