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- PDB-1krv: Galactoside Acetyltransferase in Complex with CoA and PNP-beta-Gal -

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Basic information

Entry
Database: PDB / ID: 1krv
TitleGalactoside Acetyltransferase in Complex with CoA and PNP-beta-Gal
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 / 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
4-nitrophenyl beta-D-galactopyranoside / COENZYME A / Galactoside O-acetyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: GALACTOSIDE O-ACETYLTRANSFERASE
B: GALACTOSIDE O-ACETYLTRANSFERASE
C: GALACTOSIDE O-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6879
Polymers68,4813
Non-polymers3,2066
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14860 Å2
ΔGint-39 kcal/mol
Surface area22050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.300, 183.800, 121.500
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: Sugar ChemComp-147 / 4-nitrophenyl beta-D-galactopyranoside / 1-O-[P-NITROPHENYL]-BETA-D-GALACTOPYRANOSE / 4-nitrophenyl beta-D-galactoside / 4-nitrophenyl D-galactoside / 4-nitrophenyl galactoside


Type: D-saccharide / Mass: 301.249 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C12H15NO8
IdentifierTypeProgram
1-O-[P-nitrophenyl]-b-D-galactopyranoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Ammonium sulfate, TES, tartaric acid, coenzyme A, PNP-beta-Gal, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.8 / 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 12, 1999 / 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: 2.8→31 Å / Num. all: 17605 / Num. obs: 17605 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.11
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.201 / % possible all: 69.1
Reflection
*PLUS
Num. measured all: 77286 / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
% possible obs: 69.1 % / Rmerge(I) obs: 0.201

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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: 2.8→31 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 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 861 4.9 %RANDOM
Rwork0.174 ---
all0.178 17605 --
obs0.178 17605 94.1 %-
Displacement parametersBiso mean: 20.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.8→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4752 0 207 70 5029
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.75
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.331.5
X-RAY DIFFRACTIONx_mcangle_it2.22
X-RAY DIFFRACTIONx_scbond_it2.322
X-RAY DIFFRACTIONx_scangle_it3.642.5
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.291 59 4.7 %
Rwork0.22 1202 -
obs--69.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PNP.PARPNP.TOP
X-RAY DIFFRACTION3COA.PARCOA.TOP
Refinement
*PLUS
Rfactor all: 0.178 / Rfactor obs: 0.174 / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.75
LS refinement shell
*PLUS
Rfactor Rfree: 0.291 / Rfactor Rwork: 0.22 / Rfactor obs: 0.22

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