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- PDB-1krr: Galactoside Acetyltransferase in Complex with Acetyl-Coenzyme A -

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Basic information

Entry
Database: PDB / ID: 1krr
TitleGalactoside Acetyltransferase in Complex with Acetyl-Coenzyme A
ComponentsGALACTOSIDE O-ACETYLTRANSFERASEGalactoside 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 / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / 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 / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / Galactoside O-acetyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.5 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 10, 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)70,9106
Polymers68,4813
Non-polymers2,4293
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-58 kcal/mol
Surface area25910 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 / Galactoside 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-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.65 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: Dec 2, 1998 / 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: 2.5→26 Å / Num. all: 23094 / Num. obs: 23094 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.089
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.298 / % possible all: 68.8
Reflection
*PLUS
Num. measured all: 93176 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 68.8 % / Rmerge(I) obs: 0.298

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.851refinement
X-GENdata reduction
XDSdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.5→26 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1117 4.8 %RANDOM
Rwork0.193 ---
all0.196 23094 --
obs0.196 23094 90.1 %-
Displacement parametersBiso mean: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4713 0 153 113 4979
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg3
X-RAY DIFFRACTIONx_dihedral_angle_d27
X-RAY DIFFRACTIONx_improper_angle_d0.83
X-RAY DIFFRACTIONx_mcbond_it1.271.5
X-RAY DIFFRACTIONx_mcangle_it2.072
X-RAY DIFFRACTIONx_scbond_it2.292
X-RAY DIFFRACTIONx_scangle_it3.562.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.332 81 4.7 %
Rwork0.252 1654 -
obs--68.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2ACA.PARACA.TOP
Refinement
*PLUS
Rfactor all: 0.196 / Rfactor obs: 0.193 / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.83
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / Rfactor Rfree: 0.332 / Rfactor Rwork: 0.252 / Rfactor obs: 0.252

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