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- PDB-7ml5: Structure of the Starch Branching Enzyme I (BEI) complexed with m... -

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Basic information

Entry
Database: PDB / ID: 7ml5
TitleStructure of the Starch Branching Enzyme I (BEI) complexed with maltododecaose from Oryza sativa L
ComponentsIsoform 2 of 1,4-alpha-glucan-branching enzyme, chloroplastic/amyloplastic
KeywordsTRANSFERASE/SUBSTRATE / rBEI / maltododecaose / Branching Enzyme I / TRANSFERASE / TRANSFERASE-SUBSTRATE complex
Function / homology
Function and homology information


starch metabolic process / starch biosynthetic process / amyloplast / cation binding / 1,4-alpha-glucan branching enzyme / 1,4-alpha-glucan branching enzyme activity / starch catabolic process / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds / chloroplast ...starch metabolic process / starch biosynthetic process / amyloplast / cation binding / 1,4-alpha-glucan branching enzyme / 1,4-alpha-glucan branching enzyme activity / 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 / Glycosyl hydrolase, all-beta / Immunoglobulin E-set ...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, chloroplastic/amyloplastic
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsNayebi Gavgani, H. / Fawaz, R. / Geiger, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-06ER15822 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: A structural explanation for the mechanism and specificity of plant branching enzymes I and IIb.
Authors: Gavgani, H.N. / Fawaz, R. / Ehyaei, N. / Walls, D. / Pawlowski, K. / Fulgos, R. / Park, S. / Assar, Z. / Ghanbarpour, A. / Geiger, J.H.
History
DepositionApr 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 5, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 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: Isoform 2 of 1,4-alpha-glucan-branching enzyme, chloroplastic/amyloplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7323
Polymers81,1011
Non-polymers2,6302
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.670, 80.107, 182.716
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Isoform 2 of 1,4-alpha-glucan-branching enzyme, chloroplastic/amyloplastic / Q-enzyme / Starch-branching enzyme


Mass: 81101.477 Da / Num. of mol.: 1 / Mutation: L40M, V280M, S443P, T669A
Source method: isolated from a genetically manipulated source
Details: L40M-V280M-S443P-T669A is the protein variant that produced the crystal.
Source: (gene. exp.) Oryza sativa subsp. japonica (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-(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-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1963.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,12,11/[a2122h-1a_1-5]/1-1-1-1-1-1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1_h4-i1_i4-j1_j4-k1_k4-l1WURCSPDB2Glycan 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]{[(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: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.83 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 30% PEG8K, 550 mM sodium acetate, and 100 mM sodium cacodylate (pH 6.9)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→39.97 Å / Num. obs: 28616 / % possible obs: 95.24 % / Redundancy: 4.1 % / Biso Wilson estimate: 36.88 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.7
Reflection shellResolution: 2.35→2.434 Å / Rmerge(I) obs: 0.316 / Num. unique obs: 2155 / % possible all: 73.45

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VU2

3vu2


Resolution: 2.35→39.97 Å / SU ML: 0.2826 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.5375
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 1457 5.09 %1457
Rwork0.1648 27159 --
obs0.1682 28616 95.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.32 Å2
Refinement stepCycle: LAST / Resolution: 2.35→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5488 0 178 198 5864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315878
X-RAY DIFFRACTIONf_angle_d0.61347975
X-RAY DIFFRACTIONf_chiral_restr0.2301856
X-RAY DIFFRACTIONf_plane_restr0.00391018
X-RAY DIFFRACTIONf_dihedral_angle_d15.42482171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.430.32331110.23132043X-RAY DIFFRACTION73.42
2.43-2.530.29371160.21572420X-RAY DIFFRACTION85.19
2.53-2.650.30691540.21272632X-RAY DIFFRACTION94.5
2.65-2.790.28441440.21472778X-RAY DIFFRACTION99.15
2.79-2.960.28161500.20472822X-RAY DIFFRACTION99.97
2.96-3.190.23841450.18812844X-RAY DIFFRACTION100
3.19-3.510.24641550.17332820X-RAY DIFFRACTION100
3.51-4.020.18631510.14652887X-RAY DIFFRACTION99.93
4.02-5.060.19241680.12412870X-RAY DIFFRACTION100
5.06-39.970.22161630.14273043X-RAY DIFFRACTION99.66

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