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- PDB-7xsy: Ligand free structure of branching enzyme isoform 3 (BE3) from Cr... -

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Basic information

Entry
Database: PDB / ID: 7xsy
TitleLigand free structure of branching enzyme isoform 3 (BE3) from Crocosphaera subtropica ATCC 51142
Components1,4-alpha-glucan branching enzyme
KeywordsTRANSFERASE / Starch / Cyanobacteria
Function / homology
Function and homology information


: / cation binding / 1,4-alpha-glucan branching enzyme / 1,4-alpha-glucan branching enzyme activity / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds / 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 / Glycosidases ...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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
1,4-alpha-glucan branching enzyme
Similarity search - Component
Biological speciesCrocosphaera subtropica ATCC 51142 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTamura, T. / Suzuki, E. / Suzuki, R.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K06135 Japan
Japan Society for the Promotion of Science (JSPS)16K07467 Japan
CitationJournal: To be published
Title: Ligand free structure of branching enzyme isoform 3 (BE3) from Crocosphaera subtropica ATCC 51142
Authors: Tamura, T. / Suzuki, E. / Suzuki, R.
History
DepositionMay 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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
D: 1,4-alpha-glucan branching enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,6466
Polymers310,4614
Non-polymers1842
Water6,810378
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-26 kcal/mol
Surface area94970 Å2
Unit cell
Length a, b, c (Å)148.050, 149.910, 162.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
1,4-alpha-glucan branching enzyme


Mass: 77615.367 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crocosphaera subtropica ATCC 51142 (bacteria)
Strain: ATCC 51142 / BH68 / Gene: CP000806 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B1WZK4, 1,4-alpha-glucan branching enzyme
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.04 Å3/Da / Density % sol: 59.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1 M HEPES , 0.3 M Potassium sodium tartrate, 0.2 M Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Mar 13, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→88.31 Å / Num. obs: 124975 / % possible obs: 100 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 6.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 18092 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GQU

5gqu


Resolution: 2.5→48.06 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.911 / SU B: 8.902 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.401 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26084 6476 5.2 %RANDOM
Rwork0.19669 ---
obs0.19994 118321 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.759 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.5→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20884 0 12 378 21274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01321576
X-RAY DIFFRACTIONr_bond_other_d0.0010.01718397
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.6429331
X-RAY DIFFRACTIONr_angle_other_deg1.2681.57142645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.59152521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28422.3041354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.156153262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.73515135
X-RAY DIFFRACTIONr_chiral_restr0.0730.22627
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0224637
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025068
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_it3.6844.83610132
X-RAY DIFFRACTIONr_mcbond_other3.6834.83510131
X-RAY DIFFRACTIONr_mcangle_it5.4387.24412637
X-RAY DIFFRACTIONr_mcangle_other5.4387.24412638
X-RAY DIFFRACTIONr_scbond_it3.7455.13411444
X-RAY DIFFRACTIONr_scbond_other3.7455.13411445
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6317.59716695
X-RAY DIFFRACTIONr_long_range_B_refined7.5353.9523963
X-RAY DIFFRACTIONr_long_range_B_other7.53153.94723920
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 458 -
Rwork0.249 8675 -
obs--100 %

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