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- PDB-3k1d: Crystal structure of glycogen branching enzyme synonym: 1,4-alpha... -

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Basic information

Entry
Database: PDB / ID: 3k1d
TitleCrystal structure of glycogen branching enzyme synonym: 1,4-alpha-D-glucan:1,4-alpha-D-GLUCAN 6-glucosyl-transferase from mycobacterium tuberculosis H37RV
Components1,4-alpha-glucan-branching enzyme
KeywordsTRANSFERASE / MYCOBACTERIUM TUBERCULOSIS H37Rv / MESOPHILIC HUMAN PATHOGEN / GLGB Rv1326c GENE / GLYCOSYL TRANSFERASE / N-TERMINAL SANDWIC / Glycogen biosynthesis / Glycosyltransferase
Function / homology
Function and homology information


cation binding / 1,4-alpha-glucan branching enzyme / : / 1,4-alpha-glucan branching enzyme activity / glucan biosynthetic process / capsule polysaccharide biosynthetic process / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / plasma membrane ...cation binding / 1,4-alpha-glucan branching enzyme / : / 1,4-alpha-glucan branching enzyme activity / glucan biosynthetic process / capsule polysaccharide biosynthetic process / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 / Golgi alpha-mannosidase II ...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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1,4-alpha-glucan branching enzyme GlgB / 1,4-alpha-glucan branching enzyme GlgB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsPal, K. / Kumar, S. / Swaminathan, K.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of full-length Mycobacterium tuberculosis H37Rv glycogen branching enzyme: insights of N-terminal beta-sandwich in substrate specificity and enzymatic activity
Authors: Pal, K. / Kumar, S. / Sharma, S. / Garg, S.K. / Alam, M.S. / Xu, H.E. / Agrawal, P. / Swaminathan, K.
#1: Journal: Protein Expr.Purif. / Year: 2007
Title: Expression and characterization of alpha-(1,4)-glucan branching enzyme Rv1326c of Mycobacterium tuberculosis H37Rv
Authors: Garg, S.K. / Alam, M.S. / Kishan, K.V. / Agrawal, P.
History
DepositionSep 27, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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


Theoretical massNumber of molelcules
Total (without water)80,8281
Polymers80,8281
Non-polymers00
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.373, 156.861, 48.021
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 1,4-alpha-glucan-branching enzyme / Glycogen-branching enzyme / BE / 1 / 4-alpha-D-glucan:1 / 4-alpha-D-glucan 6-glucosyl-transferase


Mass: 80828.070 Da / Num. of mol.: 1 / Fragment: RESIDUES 10-731
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: glgB, Rv1326c / Plasmid: PET29A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q10625, UniProt: P9WN45*PLUS, 1,4-alpha-glucan branching enzyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 / Wavelength: 0.9897 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2009
RadiationMonochromator: C (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978721
20.98971
ReflectionResolution: 2.33→50 Å / Num. obs: 36272 / % possible obs: 99.9 % / Redundancy: 14.4 % / Biso Wilson estimate: 27.3 Å2 / Rsym value: 0.175 / Net I/σ(I): 12.9
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 15.6 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.76 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 1M7X

1m7x


Resolution: 2.33→19.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1996027.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1800 5 %RANDOM
Rwork0.193 ---
obs0.193 36160 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.0164 Å2 / ksol: 0.365515 e/Å3
Displacement parametersBiso mean: 35.7 Å2
Baniso -1Baniso -2Baniso -3
1-8.07 Å20 Å20 Å2
2---2.58 Å20 Å2
3----5.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.33→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5724 0 0 323 6047
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.33→2.48 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.247 298 5 %
Rwork0.218 5627 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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