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- PDB-5gqz: Crystal structure of branching enzyme Y500A mutant from Cyanothec... -

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Basic information

Entry
Database: PDB / ID: 5gqz
TitleCrystal structure of branching enzyme Y500A mutant from Cyanothece sp. ATCC 51142
Components1,4-alpha-glucan branching enzyme GlgB
KeywordsTRANSFERASE / branching enzyme / glycoside hydrolase family 13 / cyanobacteria / starch
Function / homology
Function and homology information


1,4-alpha-glucan branching enzyme / 1,4-alpha-glucan branching enzyme activity / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding / 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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1,4-alpha-glucan branching enzyme GlgB
Similarity search - Component
Biological speciesCyanothece sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSuzuki, R. / Suzuki, E.
Funding support Japan, 3items
OrganizationGrant numberCountry
Shimadzu Science Foundation120003 Japan
JSPS KAKENHI15K18685 Japan
JSPS KAKENHI25440193 Japan
Citation
Journal: To be published
Title: Structural basis for substrate binding and catalysis of branching enzyme from Cyanothece sp. ATCC 51142
Authors: Hayashi, M. / Suzuki, R. / Colleoni, C. / Ball, S.G. / Fujita, N. / Suzuki, E.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Crystallization and crystallographic analysis of branching enzymes from Cyanothece sp. ATCC 51142
Authors: Hayashi, M. / Suzuki, R. / Colleoni, C. / Ball, S.G. / Fujita, N. / Suzuki, E.
History
DepositionAug 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,52014
Polymers92,5941
Non-polymers92613
Water16,015889
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-19 kcal/mol
Surface area29490 Å2
2
A: 1,4-alpha-glucan branching enzyme GlgB
hetero molecules

A: 1,4-alpha-glucan branching enzyme GlgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,04128
Polymers185,1892
Non-polymers1,85226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3730 Å2
ΔGint-26 kcal/mol
Surface area58760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.928, 133.928, 184.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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


Mass: 92594.328 Da / Num. of mol.: 1 / Mutation: Y500A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanothece sp. (strain ATCC 51142) (bacteria)
Strain: ATCC 51142 / Gene: glgB, glgB1, cce_2248 / Plasmid: pET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: B1WPM8, 1,4-alpha-glucan branching enzyme
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 889 / 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: 4.47 Å3/Da / Density % sol: 72.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: magnesium chloride, ethanol, HEPES-NaOH / PH range: 7.2 - 7.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 22, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 142937 / % possible obs: 100 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 68.4
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 11.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GQU

5gqu


Resolution: 1.85→47.35 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.662 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17915 7119 5 %RANDOM
Rwork0.15754 ---
obs0.15863 134668 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.24 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6266 0 58 889 7213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0196530
X-RAY DIFFRACTIONr_bond_other_d0.0010.025830
X-RAY DIFFRACTIONr_angle_refined_deg2.3361.9268870
X-RAY DIFFRACTIONr_angle_other_deg1.03313427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7325754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92324.068354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.154151008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7541528
X-RAY DIFFRACTIONr_chiral_restr0.160.2881
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0217437
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021657
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_it2.7132.1943019
X-RAY DIFFRACTIONr_mcbond_other2.7062.1923018
X-RAY DIFFRACTIONr_mcangle_it3.3643.2733772
X-RAY DIFFRACTIONr_mcangle_other3.3673.2753773
X-RAY DIFFRACTIONr_scbond_it4.1512.5773511
X-RAY DIFFRACTIONr_scbond_other4.152.5773511
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8993.725099
X-RAY DIFFRACTIONr_long_range_B_refined7.46320.1658297
X-RAY DIFFRACTIONr_long_range_B_other7.219.2017825
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 541 -
Rwork0.212 9834 -
obs--99.58 %

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