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- PDB-6klf: Crystal structure of branching enzyme D434A mutant from Cyanothec... -

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Basic information

Entry
Database: PDB / ID: 6klf
TitleCrystal structure of branching enzyme D434A mutant from Cyanothece sp. ATCC 51142
Components1,4-alpha-glucan branching enzyme GlgB
KeywordsTRANSFERASE / starch-producing cyanobacteria / inactive mutant
Function / homology
Function and homology information


1,4-alpha-glucan branching enzyme / 1,4-alpha-glucan branching enzyme activity / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding / cytosol
Similarity search - Function
: / alpha-1,4-glucan branching enzyme GlgB, N-terminal domain / 1,4-alpha-glucan-branching enzyme, GlgB / Glycogen branching enzyme GlgB, N-terminal Early set domain / 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 ...: / alpha-1,4-glucan branching enzyme GlgB, N-terminal domain / 1,4-alpha-glucan-branching enzyme, GlgB / Glycogen branching enzyme GlgB, N-terminal Early set domain / 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 speciesCrocosphaera subtropica ATCC 51142 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSuzuki, R. / Suzuki, E.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science18K06135 Japan
Japan Society for the Promotion of Science16K07467 Japan
Citation
Journal: Arch.Biochem.Biophys. / Year: 2021
Title: Cyanobacterial branching enzymes bind to alpha-glucan via surface binding sites
Authors: El Mannai, Y. / Deto, R. / Kuroki, M. / Suzuki, R. / Suzuki, E.
#1: Journal: J. Biol. Chem. / Year: 2017
Title: Bound Substrate in the Structure of Cyanobacterial Branching Enzyme Supports a New Mechanistic Model.
Authors: Hayashi, M. / Suzuki, R. / Colleoni, C. / Ball, S.G. / Fujita, N. / Suzuki, E.
History
DepositionJul 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author / database_2
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.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 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: 1,4-alpha-glucan branching enzyme GlgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,30411
Polymers88,5191
Non-polymers78510
Water9,098505
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-4 kcal/mol
Surface area29760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.745, 133.745, 184.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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: 88518.930 Da / Num. of mol.: 1 / Mutation: D434A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crocosphaera subtropica ATCC 51142 (bacteria)
Strain: ATCC 51142 / Gene: glgB, glgB1, cce_2248 / Plasmid: pET15b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: B1WPM8, 1,4-alpha-glucan branching enzyme
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.67 Å3/Da / Density % sol: 73.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 8%(w/v) ethanol, 0.1 M HEPES-NaOH pH 7.2, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 25, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 58556 / % possible obs: 99.8 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 18.8
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.365 / Num. unique obs: 2880 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GQX

5gqx


Resolution: 2.5→47.29 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.19524 2942 5 %RANDOM
Rwork0.15294 ---
obs0.15503 55534 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6270 0 50 505 6825
LS refinement shellResolution: 2.5→2.565 Å
RfactorNum. reflection% reflection
Rfree0.241 238 -
Rwork0.211 4031 -
obs--99.79 %

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