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- PDB-7txq: x-ray structure of the VioB N-acetyltransferase from Acinetobacte... -

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Basic information

Entry
Database: PDB / ID: 7txq
Titlex-ray structure of the VioB N-acetyltransferase from Acinetobacter baumannii in the present of TDP and Acetyl-CoenzymeA
ComponentsVioB
KeywordsTRANSFERASE / 4-amino-4 / 6-dideoxy-D-glucose / beta helix / N-acetyltransferase / Acinetobacter baumannii
Function / homology
Function and homology information


acyltransferase activity
Similarity search - Function
Sialic acid O-acyltransferase NeuD-like / PglD, N-terminal / PglD N-terminal domain / : / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
ACETYL COENZYME *A / THYMIDINE-5'-DIPHOSPHATE / VioB
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.65 Å
AuthorsHerkert, N.R. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM134643 United States
CitationJournal: Proteins / Year: 2022
Title: Structure and function of an N-acetyltransferase from the human pathogen Acinetobacter baumannii isolate BAL_212.
Authors: Herkert, N.R. / Thoden, J.B. / Holden, H.M.
History
DepositionFeb 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 20, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VioB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5645
Polymers23,3061
Non-polymers1,2584
Water3,279182
1
A: VioB
hetero molecules

A: VioB
hetero molecules

A: VioB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,69115
Polymers69,9183
Non-polymers3,77312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10780 Å2
ΔGint-47 kcal/mol
Surface area22630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.413, 97.413, 72.842
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-303-

NA

21A-304-

NA

31A-544-

HOH

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Components

#1: Protein VioB


Mass: 23305.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: vioB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: A0A334FGR6
#2: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 8 - 12% poly(ethylene glycol) 8000, 200 mM LiCl, 5 mM dTDP-4-amino-4,6-dideoxy-D-glucose, 5 mM CoA, and 100 mM MES (pH 6.0). ligands removed by soaking, then soak in 5 mM dTDP and 5 mM Acetyl-coenzymeA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Jul 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 30576 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rsym value: 0.061 / Net I/σ(I): 12
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3 / Num. unique obs: 4811 / Rsym value: 0.354 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7txp

7txp


Resolution: 1.65→33.46 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.952 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2042 1634 5.3 %RANDOM
Rwork0.1722 ---
obs0.1739 28942 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.79 Å2 / Biso mean: 15.258 Å2 / Biso min: 3.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.65→33.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 78 182 1816
Biso mean--24.1 26.72 -
Num. residues----209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131691
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171619
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.6712312
X-RAY DIFFRACTIONr_angle_other_deg1.3831.63756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8015220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.89423.14370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37615284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.952158
X-RAY DIFFRACTIONr_chiral_restr0.0720.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021855
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02322
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 144 -
Rwork0.238 2043 -
all-2187 -
obs--95.71 %

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