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- PDB-1kqa: GALACTOSIDE ACETYLTRANSFERASE IN COMPLEX WITH COENZYME A -

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Basic information

Entry
Database: PDB / ID: 1kqa
TitleGALACTOSIDE ACETYLTRANSFERASE IN COMPLEX WITH COENZYME A
ComponentsGALACTOSIDE O-ACETYLTRANSFERASE
KeywordsTRANSFERASE / LEFT-HANDED PARALLEL BETA HELIX
Function / homology
Function and homology information


galactoside O-acetyltransferase / galactoside O-acetyltransferase activity / lactose biosynthetic process / identical protein binding / cytoplasm
Similarity search - Function
Galactoside O-acetyltransferase LacA-like / Maltose/galactoside acetyltransferase / Maltose acetyltransferase hexapeptide capping motif / Maltose acetyltransferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) ...Galactoside O-acetyltransferase LacA-like / Maltose/galactoside acetyltransferase / Maltose acetyltransferase hexapeptide capping motif / Maltose acetyltransferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
COENZYME A / Galactoside O-acetyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWang, X.-G. / Olsen, L.R. / Roderick, S.L.
CitationJournal: Structure / Year: 2002
Title: Structure of the lac operon galactoside acetyltransferase.
Authors: Wang, X.G. / Olsen, L.R. / Roderick, S.L.
History
DepositionJan 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GALACTOSIDE O-ACETYLTRANSFERASE
B: GALACTOSIDE O-ACETYLTRANSFERASE
C: GALACTOSIDE O-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7846
Polymers68,4813
Non-polymers2,3033
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-57 kcal/mol
Surface area25780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.700, 182.500, 121.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a trimer.

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Components

#1: Protein GALACTOSIDE O-ACETYLTRANSFERASE / THIOGALACTOSIDE ACETYLTRANSFERASE


Mass: 22826.998 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: laca / Plasmid: ptac-85 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1
References: UniProt: P07464, galactoside O-acetyltransferase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S

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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: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Tris-HCl, beta-mercaptoethanol, ammonium sulfate, HEPES, tartaric acid, acetyl-CoA, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: Wang, X.G., (1999) Acta Crystallogr., D55, 1955.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 mg/mlprotein1drop
225 mMTris-HCl1droppH7.8
31 mMbeta-mercaptoethanol1drop
410 mMacetyl-CoA1drop
52.3 Mammonium sulfate1reservoir
60.1 MHEPES1reservoirpH7.4
70.17 ML(+)-tartaric acid1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 10, 2000 / Details: mirrors
RadiationMonochromator: Confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→99 Å / Num. all: 12072 / Num. obs: 12072 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.127
Reflection shellResolution: 3.2→3.3 Å / Rmerge(I) obs: 0.243 / % possible all: 79.4
Reflection
*PLUS
Num. measured all: 69299 / Rmerge(I) obs: 0.127
Reflection shell
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 3.3 Å / % possible obs: 79.4 % / Rmerge(I) obs: 0.243

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
X-GENdata reduction
XDSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→28 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 616 5.1 %RANDOM
Rwork0.195 ---
all0.197 12072 --
obs0.197 12072 96 %-
Displacement parametersBiso mean: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 3.2→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4713 0 144 0 4857
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.83
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.611.5
X-RAY DIFFRACTIONx_mcangle_it2.672
X-RAY DIFFRACTIONx_scbond_it2.922
X-RAY DIFFRACTIONx_scangle_it4.582.5
LS refinement shellHighest resolution: 3.2 Å / Total num. of bins used: 10 /
Num. reflection% reflection
Rwork936 -
Rfree-5.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2COA.PARCOA.TOP
Refinement
*PLUS
Rfactor all: 0.197 / Rfactor obs: 0.195 / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.83
LS refinement shell
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 3.3 Å / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.229 / Rfactor obs: 0.229

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