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- PDB-3n92: Crystal structure of TK1436, a GH57 branching enzyme from hyperth... -

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Basic information

Entry
Database: PDB / ID: 3n92
TitleCrystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose
Componentsalpha-amylase, GH57 family
KeywordsTRANSFERASE / GH57 family member / branching enzyme
Function / homology
Function and homology information


alpha-glucan biosynthetic process / 1,4-alpha-glucan branching enzyme / 1,4-alpha-glucan branching enzyme activity (using a glucosylated glycogenin as primer for glycogen synthesis) / 1,4-alpha-glucan branching enzyme activity / nucleotide binding
Similarity search - Function
1,4-alpha-glucan branching enzyme, C-terminal / Glycoside hydrolase families 57, central domain / 1,4-alpha-glucan branching enzyme MT3115-like / 1,4-alpha-glucan branching enzyme, C-terminal / immunoglobulin/albumin-binding domain-like / Families 57/38 glycoside transferase, middle domain / Glycoside hydrolase family 57, N-terminal domain / Glycosyl hydrolase family 57 / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel ...1,4-alpha-glucan branching enzyme, C-terminal / Glycoside hydrolase families 57, central domain / 1,4-alpha-glucan branching enzyme MT3115-like / 1,4-alpha-glucan branching enzyme, C-terminal / immunoglobulin/albumin-binding domain-like / Families 57/38 glycoside transferase, middle domain / Glycoside hydrolase family 57, N-terminal domain / Glycosyl hydrolase family 57 / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel / Glycoside hydrolase 38, N-terminal domain superfamily / Glycoside hydrolase families 57/38, central domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / 1,4-alpha-glucan branching enzyme TK1436
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsSantos, C.R. / Tonoli, C.C.C. / Trindade, D.M. / Betzel, C. / Takata, H. / Kuriki, T. / Kanai, T. / Imanaka, T. / Arni, R.K. / Murakami, M.T.
CitationJournal: Proteins / Year: 2011
Title: Structural basis for branching-enzyme activity of glycoside hydrolase family 57: Structure and stability studies of a novel branching enzyme from the hyperthermophilic archaeon Thermococcus Kodakaraensis KOD1.
Authors: Santos, C.R. / Tonoli, C.C. / Trindade, D.M. / Betzel, C. / Takata, H. / Kuriki, T. / Kanai, T. / Imanaka, T. / Arni, R.K. / Murakami, M.T.
History
DepositionMay 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alpha-amylase, GH57 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3482
Polymers66,1681
Non-polymers1801
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.762, 82.735, 111.899
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 alpha-amylase, GH57 family /


Mass: 66167.953 Da / Num. of mol.: 1 / Fragment: UNP residues 1-562
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: TK1436 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q5JDJ7, 1,4-alpha-glucan branching enzyme
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM sodium acetate (pH 5.5), 15% (w/v) PEG 8000, 10% (v/v) PEG 400 and 200 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 10, 2010
RadiationMonochromator: Si (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.89→66.53 Å / Num. obs: 13850 / % possible obs: 91.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 97.06 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 16.8
Reflection shellResolution: 2.89→2.96 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1331 / % possible all: 90.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UFA

1ufa


Resolution: 2.89→66.53 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.901 / SU B: 22.032 / SU ML: 0.42 / Cross valid method: THROUGHOUT / ESU R Free: 0.548 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30517 700 5.1 %RANDOM
Rwork0.21985 ---
obs0.22379 13113 91.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.708 Å2
Baniso -1Baniso -2Baniso -3
1-3.54 Å20 Å20 Å2
2---1.83 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.89→66.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4582 0 12 24 4618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224727
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9496400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3415549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29923.158247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.79515809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7751539
X-RAY DIFFRACTIONr_chiral_restr0.0960.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213671
X-RAY DIFFRACTIONr_mcbond_it0.6591.52734
X-RAY DIFFRACTIONr_mcangle_it1.2724409
X-RAY DIFFRACTIONr_scbond_it1.53431993
X-RAY DIFFRACTIONr_scangle_it2.7164.51991
LS refinement shellResolution: 2.886→2.961 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 53 -
Rwork0.309 852 -
obs--82.42 %

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