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- PDB-7vma: The X-ray crystallographic structure of amylo-alpha-1,6-glucosida... -

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Basic information

Entry
Database: PDB / ID: 7vma
TitleThe X-ray crystallographic structure of amylo-alpha-1,6-glucosidase from Thermococcus gammatolerans STB12
ComponentsAmylo-alpha-1,6-glucosidase, putative archaeal type glycogen debranching enzyme (Gde)
KeywordsHYDROLASE / Amylo-alpha-1 / 6-glucosidase
Function / homology
Function and homology information


amylo-alpha-1,6-glucosidase / amylo-alpha-1,6-glucosidase activity / carbohydrate metabolic process
Similarity search - Function
Putative glycogen debranching enzyme, N-terminal / N-terminal domain of (some) glycogen debranching enzymes / Glycogen debranching enzyme, C-terminal / Amylo-alpha-1,6-glucosidase / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
Amylo-alpha-1,6-glucosidase, putative archaeal type glycogen debranching enzyme (Gde)
Similarity search - Component
Biological speciesThermococcus gammatolerans EJ3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.804 Å
AuthorsLi, Z.F. / Ban, X.F. / Wang, Y.M. / Li, C.M. / 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 Amylo-alpha-1,6-glucosidase from Thermococcus gannatilerans STB12
Authors: Li, Z.F. / Ban, X.F. / Wang, Y.M. / Li, C.M. / Gu, Z.B.
History
DepositionOct 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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: Amylo-alpha-1,6-glucosidase, putative archaeal type glycogen debranching enzyme (Gde)
B: Amylo-alpha-1,6-glucosidase, putative archaeal type glycogen debranching enzyme (Gde)


Theoretical massNumber of molelcules
Total (without water)137,4112
Polymers137,4112
Non-polymers00
Water25214
1
A: Amylo-alpha-1,6-glucosidase, putative archaeal type glycogen debranching enzyme (Gde)

A: Amylo-alpha-1,6-glucosidase, putative archaeal type glycogen debranching enzyme (Gde)


Theoretical massNumber of molelcules
Total (without water)137,4112
Polymers137,4112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area2850 Å2
ΔGint-18 kcal/mol
Surface area45000 Å2
MethodPISA
2
B: Amylo-alpha-1,6-glucosidase, putative archaeal type glycogen debranching enzyme (Gde)

B: Amylo-alpha-1,6-glucosidase, putative archaeal type glycogen debranching enzyme (Gde)


Theoretical massNumber of molelcules
Total (without water)137,4112
Polymers137,4112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Buried area2770 Å2
ΔGint-18 kcal/mol
Surface area43480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.087, 108.087, 225.199
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Amylo-alpha-1,6-glucosidase, putative archaeal type glycogen debranching enzyme (Gde)


Mass: 68705.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus gammatolerans EJ3 (archaea)
Strain: DSM 15229 / JCM 11827 / EJ3 / Gene: gde, TGAM_1568
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C5A758, amylo-alpha-1,6-glucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 25%tertiary butanol; 0.1M Tris

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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: May 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.52→48.77 Å / Num. obs: 44230 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.3
Reflection shellResolution: 2.52→2.6 Å / Rmerge(I) obs: 0.022 / Num. unique obs: 4569

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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: predict using alpha-fold

Resolution: 2.804→38.998 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 42.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.328 1562 4.96 %RANDOM
Rwork0.244 29903 --
obs0.2483 31465 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.94 Å2 / Biso mean: 94.3893 Å2 / Biso min: 57.17 Å2
Refinement stepCycle: final / Resolution: 2.804→38.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9704 0 0 14 9718
Biso mean---82.41 -
Num. residues----1240
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.804-2.89450.43371240.35262692281699
2.8945-2.99790.40161250.345827402865100
2.9979-3.11790.40691490.348927022851100
3.1179-3.25970.40741530.336226872840100
3.2597-3.43150.38981370.327227212858100
3.4315-3.64630.40611560.303527342890100
3.6463-3.92760.38171530.284726922845100
3.9276-4.32240.35141140.251627562870100
4.3224-4.94680.32551730.223926962869100
4.9468-6.22840.35441330.231127462879100
6.2284-38.99150.22361450.17522737288299

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