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- PDB-9u77: Crystal structure of Glycogen branching enzyme (VvGBE) from Vibri... -

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Basic information

Entry
Database: PDB / ID: 9u77
TitleCrystal structure of Glycogen branching enzyme (VvGBE) from Vibrio vulnificus MO6-24/O
Components1,4-alpha-glucan branching enzyme GlgB
KeywordsTRANSFERASE / glycogen branching enzyme / GH13_9
Function / homology
Function and homology information


cation binding / 1,4-alpha-glucan branching enzyme / 1,4-alpha-glucan branching enzyme activity / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds / 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 speciesVibrio vulnificus MO6-24/O (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAn, Y. / Lee, S.J. / Park, J.T. / Woo, E.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural characterization of glycogen branching enzyme (VvGBE) from Vibrio vulnificus
Authors: An, Y. / Lee, S.J. / Park, J.T. / Woo, E.J.
History
DepositionMar 24, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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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
B: 1,4-alpha-glucan branching enzyme GlgB


Theoretical massNumber of molelcules
Total (without water)170,2792
Polymers170,2792
Non-polymers00
Water4,576254
1
A: 1,4-alpha-glucan branching enzyme GlgB


Theoretical massNumber of molelcules
Total (without water)85,1401
Polymers85,1401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1,4-alpha-glucan branching enzyme GlgB


Theoretical massNumber of molelcules
Total (without water)85,1401
Polymers85,1401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.800, 106.063, 141.126
Angle α, β, γ (deg.)90.000, 123.300, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-905-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 26 - 742 / Label seq-ID: 26 - 742

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.85162549142, -0.495704843979, -0.170325365167), (0.494281627632, -0.867640127936, 0.053724119171), (-0.174412427736, -0.0384358693319, 0.983922247436)Vector: -72. ...NCS oper: (Code: given
Matrix: (-0.85162549142, -0.495704843979, -0.170325365167), (0.494281627632, -0.867640127936, 0.053724119171), (-0.174412427736, -0.0384358693319, 0.983922247436)
Vector: -72.3119736208, -5.14143957709, 16.0645075697)

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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: 85139.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus MO6-24/O (bacteria) / Strain: MO6-24/O / Gene: glgB, CRN52_00655 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A2S3R8T2, 1,4-alpha-glucan branching enzyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 3350, 0.1M BIS-TRIS pH 6.5, 0.2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 17, 2019
RadiationProtocol: 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: 70034 / % possible obs: 99.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 48.35 Å2 / Rrim(I) all: 0.211 / Rsym value: 0.194 / Net I/σ(I): 24.1
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 3467 / Rsym value: 0.93 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→49.31 Å / SU ML: 0.379 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.6637
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2567 1981 2.87 %
Rwork0.2157 67085 -
obs0.2169 69066 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.99 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11642 0 0 254 11896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002512028
X-RAY DIFFRACTIONf_angle_d0.602116362
X-RAY DIFFRACTIONf_chiral_restr0.04621634
X-RAY DIFFRACTIONf_plane_restr0.00352150
X-RAY DIFFRACTIONf_dihedral_angle_d4.45781578
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.00241867077 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.36531200.3343840X-RAY DIFFRACTION78.06
2.56-2.630.3661340.30194789X-RAY DIFFRACTION97.2
2.63-2.710.33641440.28224777X-RAY DIFFRACTION97.41
2.71-2.80.35361420.28084837X-RAY DIFFRACTION97.55
2.8-2.890.33971290.27714813X-RAY DIFFRACTION97.63
2.89-3.010.32571500.26614842X-RAY DIFFRACTION98.56
3.01-3.150.3371410.25034890X-RAY DIFFRACTION98.67
3.15-3.310.25321400.23394907X-RAY DIFFRACTION99.19
3.31-3.520.31551480.22244878X-RAY DIFFRACTION99.17
3.52-3.790.22161500.2064855X-RAY DIFFRACTION98.14
3.79-4.170.2581400.18794897X-RAY DIFFRACTION99.25
4.17-4.780.1971450.17424910X-RAY DIFFRACTION98.96
4.78-6.020.22441460.18644879X-RAY DIFFRACTION98.24
6.02-49.310.20491520.19174971X-RAY DIFFRACTION97.94
Refinement TLS params.Method: refined / Origin x: -38.6709603333 Å / Origin y: -17.4254318418 Å / Origin z: 16.1998270254 Å
111213212223313233
T0.404332386905 Å20.00648089903869 Å20.0128296749322 Å2-0.334718178819 Å2-0.000187201470959 Å2--0.415550798035 Å2
L0.521123941448 °2-0.247284280651 °20.198568718578 °2-0.212148810861 °2-0.0757772738805 °2--0.265701995538 °2
S0.0482264966273 Å °0.0647471921432 Å °0.047755437867 Å °-0.0722469435557 Å °-0.0214433008695 Å °0.00417517219625 Å °-0.0169921902269 Å °0.0167733638273 Å °-0.0230381454331 Å °
Refinement TLS groupSelection details: all

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