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- PDB-7eav: The X-ray crystallographic structure of glycogen debranching enzy... -

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Basic information

Entry
Database: PDB / ID: 7eav
TitleThe X-ray crystallographic structure of glycogen debranching enzyme from Sulfolobus solfataricus STB09
ComponentsGlycogen debranching enzyme
KeywordsHYDROLASE / Glycogen Debranching Enzyme
Function / homology
Function and homology information


glycogen debranching enzyme activity / glycogen catabolic process / aminopeptidase activity / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycogen debranching enzyme, GlgX type / Glycogen debranching enzyme GlgX/isoamylase, N-terminal Early set domain / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Glycogen debranching enzyme
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsLi, Z.F. / Ban, X.F. / Tian, Y.X. / Li, C.M. / Cheng, L. / Hong, Y. / Gu, Z.B.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31722040 China
National Natural Science Foundation of China (NSFC)31771935 China
National Natural Science Foundation of China (NSFC)31901628 China
CitationJournal: To Be Published
Title: The X-ray Crystallographic Structure of Debranching Enzyme from Sulfolobus solfataricus STB09
Authors: Li, Z.F. / Ban, X.F. / Tian, Y.X. / Li, C.M. / Gu, Z.B.
History
DepositionMar 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: 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

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Assembly

Deposited unit
A: Glycogen debranching enzyme
B: Glycogen debranching enzyme


Theoretical massNumber of molelcules
Total (without water)166,3642
Polymers166,3642
Non-polymers00
Water3,243180
1
A: Glycogen debranching enzyme
B: Glycogen debranching enzyme

A: Glycogen debranching enzyme
B: Glycogen debranching enzyme

A: Glycogen debranching enzyme
B: Glycogen debranching enzyme


Theoretical massNumber of molelcules
Total (without water)499,0916
Polymers499,0916
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area22480 Å2
ΔGint-66 kcal/mol
Surface area142360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.543, 203.543, 89.466
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Glycogen debranching enzyme / Glycogen debranching enzyme GlgX / Glycogen operon protein GlgX


Mass: 83181.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (archaea)
Gene: orf c06021, glgX, SSOP1_2225, SULA_2828, SULB_2829, SULC_2826, SULG_14405, SULH_14405, SULI_14405, SULM_14335, SULN_14325, SULO_14345, SULZ_14425
Production host: Escherichia coli (E. coli) / References: UniProt: P95868
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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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: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3000,lithium sulfate, imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 52466 / % possible obs: 99.9 % / Redundancy: 11.8 % / Rpim(I) all: 0.162 / Net I/σ(I): 6.4
Reflection shellResolution: 2.8→2.89 Å / Num. unique obs: 4530 / CC1/2: 0.595

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIX1.14_3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vr5

2vr5


Resolution: 2.803→49.113 Å / SU ML: 0.73 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 42.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3252 2584 4.98 %RANDOM
Rwork0.2644 49334 --
obs0.2674 51918 98.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.36 Å2 / Biso mean: 61.0181 Å2 / Biso min: 23.33 Å2
Refinement stepCycle: final / Resolution: 2.803→49.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11692 0 0 180 11872
Biso mean---47.45 -
Num. residues----1429
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.803-2.85650.47981480.4489267598
2.8565-2.91480.47751490.4419269398
2.9148-2.97820.48071290.4337269798
2.9782-3.04750.48511340.4213270298
3.0475-3.12370.46841710.4179264798
3.1237-3.20810.46941590.4081268998
3.2081-3.30250.49511240.3803274699
3.3025-3.40910.36861270.3594271599
3.4091-3.53090.39411570.3318272699
3.5309-3.67220.36681190.2989274199
3.6722-3.83930.3541490.2677275499
3.8393-4.04160.33661290.258277599
4.0416-4.29470.28721370.23072760100
4.2947-4.6260.27791460.19192750100
4.626-5.09110.24861400.17772785100
5.0911-5.82680.23831570.18782780100
5.8268-7.33720.28141620.20552805100
7.3372-49.1130.2051470.1754289499

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