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- PDB-5clw: Crystal structure of human glycogen branching enzyme (GBE1) in co... -

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Basic information

Entry
Database: PDB / ID: 5clw
TitleCrystal structure of human glycogen branching enzyme (GBE1) in complex with maltoheptaose
Components1,4-alpha-glucan-branching enzyme
KeywordsTRANSFERASE / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Glycogen storage disease type IV (GBE1) / cation binding / 1,4-alpha-glucan branching enzyme / : / 1,4-alpha-glucan branching enzyme activity / glycogen biosynthetic process / glycogen metabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycogen synthesis / generation of precursor metabolites and energy ...Glycogen storage disease type IV (GBE1) / cation binding / 1,4-alpha-glucan branching enzyme / : / 1,4-alpha-glucan branching enzyme activity / glycogen biosynthetic process / glycogen metabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycogen synthesis / 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 / molecular replacement / Resolution: 2.8 Å
AuthorsKrojer, T. / Froese, D.S. / Goubin, S. / Strain-Damerell, C. / Mahajan, P. / Burgess-Brown, N. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. ...Krojer, T. / Froese, D.S. / Goubin, S. / Strain-Damerell, C. / Mahajan, P. / Burgess-Brown, N. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Yue, W. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Crystal structure of human glycogen branching enzyme (GBE1) in complex with maltoheptaose
Authors: Krojer, T. / Froese, D.S. / Goubin, S. / Strain-Damerell, C. / Mahajan, P. / Burgess-Brown, N. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Yue, W. / Structural Genomics Consortium (SGC)
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,5927
Polymers231,1103
Non-polymers3,4824
Water3,081171
1
A: 1,4-alpha-glucan-branching enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1902
Polymers77,0371
Non-polymers1,1531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1,4-alpha-glucan-branching enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2133
Polymers77,0371
Non-polymers1,1762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 1,4-alpha-glucan-branching enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1902
Polymers77,0371
Non-polymers1,1531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.689, 164.536, 313.208
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


Mass: 77036.742 Da / Num. of mol.: 3 / Fragment: UNP residues 38-700
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GBE1 / Plasmid: pFB-LIC-Bse / Production host: unidentified baculovirus
References: UniProt: Q04446, 1,4-alpha-glucan branching enzyme
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,7,6/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 3.25 Å3/Da / Density % sol: 62.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 17% PEG 3350 , 0.2M sodium succinate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→313.21 Å / Num. obs: 74191 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 73.53 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.8-3.134.70.7582.197113208760.6930.38499.8
6.26-313.214.30.05222.73003069240.9960.02899.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
Aimless0.1.29data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bzy

4bzy


Resolution: 2.8→156.6 Å / Cor.coef. Fo:Fc: 0.9271 / Cor.coef. Fo:Fc free: 0.9 / SU R Cruickshank DPI: 0.665 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.608 / SU Rfree Blow DPI: 0.29 / SU Rfree Cruickshank DPI: 0.299
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 3710 5 %RANDOM
Rwork0.1952 ---
obs0.197 74138 99.69 %-
Displacement parametersBiso mean: 55.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.1505 Å20 Å20 Å2
2--3.2452 Å20 Å2
3----4.3957 Å2
Refine analyzeLuzzati coordinate error obs: 0.364 Å
Refinement stepCycle: LAST / Resolution: 2.8→156.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15458 0 235 171 15864
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0116188HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0721993HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5418SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes346HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2374HARMONIC5
X-RAY DIFFRACTIONt_it16188HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion18.55
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2038SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact18063SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2924 267 4.94 %
Rwork0.2514 5139 -
all0.2534 5406 -
obs--99.67 %

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