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- PDB-3vu2: Structure of the Starch Branching Enzyme I (BEI) complexed with m... -

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Basic information

Entry
Database: PDB / ID: 3vu2
TitleStructure of the Starch Branching Enzyme I (BEI) complexed with maltopentaose from Oryza sativa L
Components1,4-alpha-glucan-branching enzyme, chloroplastic/amyloplastic
KeywordsTRANSFERASE / Carbohydrate-binding module 48
Function / homology
Function and homology information


starch metabolic process / starch biosynthetic process / amyloplast / 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 / starch catabolic process / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds ...starch metabolic process / starch biosynthetic process / amyloplast / 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 / starch catabolic process / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds / chloroplast / carbohydrate metabolic process / 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
alpha-maltopentaose / beta-D-glucopyranose / 1,4-alpha-glucan-branching enzyme, chloroplastic/amyloplastic
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsChaen, K. / Kakuta, Y. / Kimura, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2012
Title: Crystal structure of the rice branching enzyme I (BEI) in complex with maltopentaose.
Authors: Chaen, K. / Noguchi, J. / Omori, T. / Kakuta, Y. / Kimura, M.
History
DepositionJun 14, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / 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.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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, chloroplastic/amyloplastic
B: 1,4-alpha-glucan-branching enzyme, chloroplastic/amyloplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,24213
Polymers162,4032
Non-polymers2,83911
Water14,178787
1
A: 1,4-alpha-glucan-branching enzyme, chloroplastic/amyloplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4835
Polymers81,2021
Non-polymers1,2814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 1,4-alpha-glucan-branching enzyme, chloroplastic/amyloplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7598
Polymers81,2021
Non-polymers1,5577
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.810, 66.560, 169.625
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 1,4-alpha-glucan-branching enzyme, chloroplastic/amyloplastic / Q-enzyme / Starch-branching enzyme


Mass: 81201.578 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 66-767 / Mutation: E399Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: SBE1, RBE1, Os06g0726400, LOC_Os06g51084, P0017G10.8-1, P0017G10.8-2, P0548E04.28-1, P0548E04.28-2
Production host: Escherichia coli (E. coli)
References: UniProt: Q01401, 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 / alpha-maltopentaose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltopentaose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 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]{}}}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 787 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.06 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 72156 / Num. obs: 72156 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→37.22 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.337 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.447 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28641 3563 5.1 %RANDOM
Rwork0.22607 ---
obs0.22908 66961 87.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.23→37.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11275 0 190 787 12252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02111882
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0161.94616109
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3551399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31323.483623
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.651151903
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4441577
X-RAY DIFFRACTIONr_chiral_restr0.0750.21655
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219245
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.451.56902
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.792211119
X-RAY DIFFRACTIONr_scbond_it0.5834980
X-RAY DIFFRACTIONr_scangle_it1.0424.54981
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.234→2.292 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.841 36 -
Rwork0.812 678 -
obs--12.21 %

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