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- PDB-4bzy: Crystal structure of human glycogen branching enzyme (GBE1) -

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Basic information

Entry
Database: PDB / ID: 4bzy
TitleCrystal structure of human glycogen branching enzyme (GBE1)
Components1,4-ALPHA-GLUCAN-BRANCHING ENZYME
KeywordsTRANSFERASE
Function / homology
Function and homology information


Glycogen storage disease type IV (GBE1) / 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 / glycogen metabolic process / Glycogen synthesis / hydrolase activity, hydrolyzing O-glycosyl compounds / generation of precursor metabolites and energy ...Glycogen storage disease type IV (GBE1) / 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 / glycogen metabolic process / Glycogen synthesis / hydrolase activity, hydrolyzing O-glycosyl compounds / generation of precursor metabolites and energy / carbohydrate binding / negative regulation of neuron apoptotic process / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1,4-alpha-glucan-branching enzyme
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsFroese, D.S. / Krojer, T. / Goubin, S. / Strain-Damerell, C. / Mahajan, P. / von Delft, F. / Burgess-Brown, N. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Yue, W.W.
CitationJournal: Hum.Mol.Genet. / Year: 2015
Title: Structural Basis of Glycogen Branching Enzyme Deficiency and Pharmacologic Rescue by Rational Peptide Design.
Authors: Froese, D.S. / Michaeli, A. / Mccorvie, T.J. / Krojer, T. / Sasi, M. / Melaev, E. / Goldblum, A. / Zatsepin, M. / Lossos, A. / Alvarez, R. / Escriba, P.V. / Minaissan, B.A. / von Delft, F. / ...Authors: Froese, D.S. / Michaeli, A. / Mccorvie, T.J. / Krojer, T. / Sasi, M. / Melaev, E. / Goldblum, A. / Zatsepin, M. / Lossos, A. / Alvarez, R. / Escriba, P.V. / Minaissan, B.A. / von Delft, F. / Kakhlon, O. / Yue, W.W.
History
DepositionJul 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Oct 7, 2015Group: Database references
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BF" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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
B: 1,4-ALPHA-GLUCAN-BRANCHING ENZYME
C: 1,4-ALPHA-GLUCAN-BRANCHING ENZYME


Theoretical massNumber of molelcules
Total (without water)241,6373
Polymers241,6373
Non-polymers00
Water10,989610
1
A: 1,4-ALPHA-GLUCAN-BRANCHING ENZYME


Theoretical massNumber of molelcules
Total (without water)80,5461
Polymers80,5461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 1,4-ALPHA-GLUCAN-BRANCHING ENZYME


Theoretical massNumber of molelcules
Total (without water)80,5461
Polymers80,5461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 1,4-ALPHA-GLUCAN-BRANCHING ENZYME


Theoretical massNumber of molelcules
Total (without water)80,5461
Polymers80,5461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.278, 164.538, 311.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 1,4-ALPHA-GLUCAN-BRANCHING ENZYME / BRANCHER ENZYME / GLYCOGEN-BRANCHING ENZYME / GBE1


Mass: 80545.703 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q04446, 1,4-alpha-glucan branching enzyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 610 / 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: 3.18 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growDetails: 22% PEG 3350, 0.05M SODIUM SUCCINATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.75→91.3 Å / Num. obs: 78285 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 18.1 % / Biso Wilson estimate: 48.75 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 16.3
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AMK

3amk


Resolution: 2.75→91.303 Å / SU ML: 0.32 / σ(F): 1.36 / Phase error: 23.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 3909 5 %
Rwork0.1845 --
obs0.1865 78216 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→91.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15453 0 0 610 16063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315951
X-RAY DIFFRACTIONf_angle_d0.75921638
X-RAY DIFFRACTIONf_dihedral_angle_d12.9985656
X-RAY DIFFRACTIONf_chiral_restr0.032202
X-RAY DIFFRACTIONf_plane_restr0.0042801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7501-2.78360.34341340.26812585X-RAY DIFFRACTION98
2.7836-2.81890.31581370.26112647X-RAY DIFFRACTION100
2.8189-2.85590.30361450.2512607X-RAY DIFFRACTION100
2.8559-2.89510.29781230.24692662X-RAY DIFFRACTION100
2.8951-2.93640.29041340.24482645X-RAY DIFFRACTION100
2.9364-2.98030.32231280.23492632X-RAY DIFFRACTION100
2.9803-3.02680.24111270.23752620X-RAY DIFFRACTION100
3.0268-3.07650.28561510.22592637X-RAY DIFFRACTION100
3.0765-3.12950.25341450.22042604X-RAY DIFFRACTION100
3.1295-3.18640.28081310.21372639X-RAY DIFFRACTION99
3.1864-3.24770.25391550.20462651X-RAY DIFFRACTION100
3.2477-3.3140.24171450.2122594X-RAY DIFFRACTION100
3.314-3.38610.261340.20392658X-RAY DIFFRACTION100
3.3861-3.46480.28481490.20462655X-RAY DIFFRACTION100
3.4648-3.55150.24191310.19912640X-RAY DIFFRACTION100
3.5515-3.64750.23351160.19462653X-RAY DIFFRACTION100
3.6475-3.75490.23941740.18792642X-RAY DIFFRACTION100
3.7549-3.87610.22031550.18032624X-RAY DIFFRACTION100
3.8761-4.01460.20061580.16892639X-RAY DIFFRACTION100
4.0146-4.17530.20631260.15572672X-RAY DIFFRACTION100
4.1753-4.36540.21091440.13952672X-RAY DIFFRACTION100
4.3654-4.59550.16851250.14322666X-RAY DIFFRACTION100
4.5955-4.88340.1571500.13872637X-RAY DIFFRACTION99
4.8834-5.26040.18491530.14752658X-RAY DIFFRACTION100
5.2604-5.78970.22821310.16142684X-RAY DIFFRACTION100
5.7897-6.62730.19841490.17842712X-RAY DIFFRACTION100
6.6273-8.34880.1791220.19182763X-RAY DIFFRACTION100
8.3488-91.35290.20821370.18092809X-RAY DIFFRACTION98

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