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- PDB-6joy: The X-ray Crystallographic Structure of Branching Enzyme from Rho... -

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Basic information

Entry
Database: PDB / ID: 6joy
TitleThe X-ray Crystallographic Structure of Branching Enzyme from Rhodothermus obamensis STB05
Components1,4-alpha-glucan branching enzyme GlgB
KeywordsCARBOHYDRATE / branching enzyme
Function / homology
Function and homology information


1,4-alpha-glucan branching enzyme / 1,4-alpha-glucan branching enzyme activity (using a glucosylated glycogenin as primer for glycogen synthesis) / 1,4-alpha-glucan branching enzyme activity / cation binding / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycogen branching enzyme GlgB, N-terminal Early set domain / 1,4-alpha-glucan-branching enzyme, GlgB / 1,4-alpha-glucan-branching enzyme / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain ...Glycogen branching enzyme GlgB, N-terminal Early set domain / 1,4-alpha-glucan-branching enzyme, GlgB / 1,4-alpha-glucan-branching enzyme / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta 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
1,4-alpha-glucan branching enzyme GlgB
Similarity search - Component
Biological speciesRhodothermus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.392 Å
AuthorsLi, Z.F. / Ban, X.F. / Jiang, H.M. / Wang, Z. / Jin, T.C. / Li, C.M. / Gu, Z.B.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31722040 China
National Natural Science Foundation of China31771935 China
Citation
Journal: J.Agric.Food Chem. / Year: 2021
Title: Flexible Loop in Carbohydrate-Binding Module 48 Allosterically Modulates Substrate Binding of the 1,4-alpha-Glucan Branching Enzyme.
Authors: Jiang, H. / Xie, X. / Ban, X. / Gu, Z. / Cheng, L. / Hong, Y. / Li, C. / Li, Z.
#1: Journal: Protein Expr.Purif. / Year: 2019
Title: Expression and characterization of an extremely thermophilic 1,4-alpha-glucan branching enzyme from Rhodothermus obamensis STB05.
Authors: Wang, Z. / Xin, C. / Li, C. / Gu, Z. / Cheng, L. / Hong, Y. / Ban, X. / Li, Z.
History
DepositionMar 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1,4-alpha-glucan branching enzyme GlgB


Theoretical massNumber of molelcules
Total (without water)72,3251
Polymers72,3251
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.671, 125.671, 205.387
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein 1,4-alpha-glucan branching enzyme GlgB / 1 / 4-alpha-D-glucan:1 / 4-alpha-D-glucan 6-glucosyl-transferase / Alpha-(1->4)-glucan branching ...1 / 4-alpha-D-glucan:1 / 4-alpha-D-glucan 6-glucosyl-transferase / Alpha-(1->4)-glucan branching enzyme / Glycogen branching enzyme / BE


Mass: 72325.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodothermus marinus (bacteria) / Gene: glgB / Production host: Escherichia coli (E. coli)
References: UniProt: Q93HU3, 1,4-alpha-glucan branching enzyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 5.61 Å3/Da / Density % sol: 78.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, HEPES, ammonia sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 2.39→31.418 Å / Num. obs: 63390 / % possible obs: 96.74 % / Redundancy: 5 % / Net I/σ(I): 2
Reflection shellResolution: 2.39→10 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
HKL-3000data scaling
PHENIXphasing
RefinementResolution: 2.392→31.418 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.33
RfactorNum. reflection% reflection
Rfree0.2775 3205 5.06 %
Rwork0.2467 --
obs0.2482 63390 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.392→31.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5132 0 0 156 5288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095336
X-RAY DIFFRACTIONf_angle_d1.1147280
X-RAY DIFFRACTIONf_dihedral_angle_d4.2683003
X-RAY DIFFRACTIONf_chiral_restr0.06698
X-RAY DIFFRACTIONf_plane_restr0.007945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3922-2.42790.36921100.36241999X-RAY DIFFRACTION75
2.4279-2.46580.35321250.35072274X-RAY DIFFRACTION85
2.4658-2.50620.33361310.31882505X-RAY DIFFRACTION95
2.5062-2.54940.34731460.29742566X-RAY DIFFRACTION97
2.5494-2.59580.31831320.27792649X-RAY DIFFRACTION99
2.5958-2.64570.281570.27622665X-RAY DIFFRACTION100
2.6457-2.69970.29721550.26662642X-RAY DIFFRACTION100
2.6997-2.75830.32391540.26172642X-RAY DIFFRACTION100
2.7583-2.82240.31561340.2552668X-RAY DIFFRACTION100
2.8224-2.8930.30641230.26242692X-RAY DIFFRACTION100
2.893-2.97110.29251440.26852686X-RAY DIFFRACTION100
2.9711-3.05850.34941640.27012661X-RAY DIFFRACTION100
3.0585-3.15710.32831450.26832686X-RAY DIFFRACTION100
3.1571-3.26990.29131540.25472650X-RAY DIFFRACTION100
3.2699-3.40060.29071410.25632700X-RAY DIFFRACTION100
3.4006-3.55520.24551460.24822685X-RAY DIFFRACTION99
3.5552-3.74230.24881190.23652698X-RAY DIFFRACTION99
3.7423-3.97640.29181270.23282710X-RAY DIFFRACTION99
3.9764-4.28270.26531320.22482702X-RAY DIFFRACTION99
4.2827-4.71240.21951300.21392715X-RAY DIFFRACTION98
4.7124-5.39130.24521550.22052681X-RAY DIFFRACTION97
5.3913-6.78130.30151410.25782669X-RAY DIFFRACTION96
6.7813-31.42040.25441400.24172640X-RAY DIFFRACTION89

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