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- PDB-8sdb: Crystal Structure of E.Coli Branching Enzyme in complex with malt... -

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Basic information

Entry
Database: PDB / ID: 8sdb
TitleCrystal Structure of E.Coli Branching Enzyme in complex with malto-octose
Components1,4-alpha-glucan branching enzyme GlgB
KeywordsTRANSFERASE/CARBOHYDRATE / branching enzyme / starch / E. coli branching enzyme / SUGAR BINDING PROTEIN / TRANSFERASE-CARBOHYDRATE complex
Function / homology
Function and homology information


cation binding / 1,4-alpha-glucan branching enzyme / : / 1,4-alpha-glucan branching enzyme activity / starch metabolic process / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds / DNA damage response / cytoplasm / cytosol
Similarity search - Function
Glycogen branching enzyme GlgB, N-terminal Early set domain / 1,4-alpha-glucan-branching enzyme, GlgB / 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 ...Glycogen branching enzyme GlgB, N-terminal Early set domain / 1,4-alpha-glucan-branching enzyme, GlgB / 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
alpha-D-glucopyranose / 1,4-alpha-glucan branching enzyme GlgB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBingham, C.R. / Nayebi, H. / Fawaz, R. / Geiger, J.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB) United States
Department of Energy (DOE, United States) United States
CitationJournal: Molecules / Year: 2023
Title: The Structure of Maltooctaose-Bound Escherichia coli Branching Enzyme Suggests a Mechanism for Donor Chain Specificity.
Authors: Fawaz, R. / Bingham, C. / Nayebi, H. / Chiou, J. / Gilbert, L. / Park, S.H. / Geiger, J.H.
History
DepositionApr 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_validate_planes
Item: _pdbx_validate_planes.type

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


Theoretical massNumber of molelcules
Total (without water)292,76120
Polymers285,3394
Non-polymers7,42216
Water00
1
A: 1,4-alpha-glucan branching enzyme GlgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3798
Polymers71,3351
Non-polymers3,0457
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 1,4-alpha-glucan branching enzyme GlgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0196
Polymers71,3351
Non-polymers2,6845
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 1,4-alpha-glucan branching enzyme GlgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8484
Polymers71,3351
Non-polymers1,5133
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 1,4-alpha-glucan branching enzyme GlgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5152
Polymers71,3351
Non-polymers1801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)146.489, 146.489, 294.920
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#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 / BE


Mass: 71334.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glgB, b3432, JW3395 / Production host: Escherichia coli (E. coli)
References: UniProt: P07762, 1,4-alpha-glucan branching enzyme

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Sugars , 6 types, 16 molecules

#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


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 3 / Source method: isolated from a natural source
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: 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: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#5: 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.: 1 / Source method: isolated from a natural 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
#6: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 3 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#7: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

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: 3.2 Å3/Da / Density % sol: 61.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.3 M ammonium tartrate, pH 7.6, 10% PEG 4k

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Apr 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3→38.85 Å / Num. obs: 71397 / % possible obs: 96.16 % / Redundancy: 3.2 % / Biso Wilson estimate: 83.31 Å2 / CC1/2: 0.85 / Net I/σ(I): 12.46
Reflection shellResolution: 3→3.107 Å / Mean I/σ(I) obs: 2.55 / Num. unique obs: 5917 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→38.85 Å / SU ML: 0.4831 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.075
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3154 3616 5.07 %
Rwork0.2138 67665 -
obs0.2189 71281 96.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.29 Å2
Refinement stepCycle: LAST / Resolution: 3→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18880 0 500 0 19380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012219991
X-RAY DIFFRACTIONf_angle_d1.35627168
X-RAY DIFFRACTIONf_chiral_restr0.35192818
X-RAY DIFFRACTIONf_plane_restr0.00793464
X-RAY DIFFRACTIONf_dihedral_angle_d27.90427275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.040.38441220.31032005X-RAY DIFFRACTION74.87
3.04-3.080.39431290.29232156X-RAY DIFFRACTION82.34
3.08-3.120.37961300.2932410X-RAY DIFFRACTION89.72
3.12-3.170.34721430.28672595X-RAY DIFFRACTION97.47
3.17-3.220.44171390.30672625X-RAY DIFFRACTION99.25
3.22-3.270.36931440.29812665X-RAY DIFFRACTION99.54
3.27-3.330.36461390.28112687X-RAY DIFFRACTION99.33
3.33-3.390.3711500.27362607X-RAY DIFFRACTION99.07
3.39-3.460.32031340.25392669X-RAY DIFFRACTION98.8
3.46-3.530.33181310.25882670X-RAY DIFFRACTION99.47
3.53-3.60.37681350.26922647X-RAY DIFFRACTION98.65
3.6-3.690.45051240.34372391X-RAY DIFFRACTION88.49
3.69-3.780.43871260.29852452X-RAY DIFFRACTION91
3.78-3.880.3231340.23992581X-RAY DIFFRACTION95.83
3.88-40.30651360.22912473X-RAY DIFFRACTION92.62
4-4.120.27761440.1852678X-RAY DIFFRACTION99.26
4.12-4.270.27531330.1792695X-RAY DIFFRACTION99.33
4.27-4.440.29821420.16342681X-RAY DIFFRACTION99.33
4.44-4.640.21971360.16192685X-RAY DIFFRACTION99.33
4.64-4.890.25721320.15832729X-RAY DIFFRACTION99.62
4.89-5.190.27061740.16352674X-RAY DIFFRACTION99.72
5.19-5.590.27961550.1772718X-RAY DIFFRACTION99.76
5.59-6.150.29221180.17992756X-RAY DIFFRACTION99.79
6.15-7.040.29661520.20652758X-RAY DIFFRACTION99.79
7.04-8.850.36511600.20182772X-RAY DIFFRACTION100
8.85-38.850.29411540.20182886X-RAY DIFFRACTION98.8

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