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- PDB-7txs: X-ray structure of the VioB N-aetyltransferase from Acinetobacter... -

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Basic information

Entry
Database: PDB / ID: 7txs
TitleX-ray structure of the VioB N-aetyltransferase from Acinetobacter baumannii in the presence of a reaction intermediate
ComponentsVioB
KeywordsTRANSFERASE / 4-amino-4 / 6-dideoxy-D-glucose / beta helix / Acinetobacter baumannii / N-acetyltransferase
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
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.25 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

Downloads & links

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Assembly

Deposited unit
A: VioB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7396
Polymers23,3061
Non-polymers1,4335
Water5,080282
1
A: VioB
hetero molecules

A: VioB
hetero molecules

A: VioB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,21618
Polymers69,9183
Non-polymers4,29915
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 area7380 Å2
ΔGint-78 kcal/mol
Surface area22750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.884, 97.884, 72.959
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-302-

NA

21A-303-

NA

31A-599-

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 (E. coli) / Strain (production host): rosetta2(DE3) / References: UniProt: A0A334FGR6
#2: Chemical ChemComp-NH9 / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methyl (3R)-4-({3-[(2-{[(1S)-1-{[(2R,3S,4S,5R,6R)-4,5-dihydroxy-6-{[(R)-hydroxy{[(R)-hydroxy{[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)oxolan-2-yl]methoxy}phosphoryl]oxy}phosphoryl]oxy}-2-methyloxan-3-yl]amino}ethyl]sulfanyl}ethyl)amino]-3-oxopropyl}amino)-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate (non-preferred name)


Mass: 1340.916 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H65N10O30P5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.89 Å3/Da / Density % sol: 57.38 %
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).

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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: Aug 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 70527 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.061 / Net I/σ(I): 12.2
Reflection shellResolution: 1.25→1.35 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3 / Num. unique obs: 14096 / Rsym value: 0.302 / % possible all: 94.5

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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: 1.25→29.35 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.609 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1655 3619 5.1 %RANDOM
Rwork0.1517 ---
obs0.1524 66908 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.52 Å2 / Biso mean: 11.991 Å2 / Biso min: 4.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.25→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 89 283 1928
Biso mean--12.85 27.08 -
Num. residues----209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131743
X-RAY DIFFRACTIONr_bond_other_d00.0171666
X-RAY DIFFRACTIONr_angle_refined_deg1.821.7012396
X-RAY DIFFRACTIONr_angle_other_deg1.4641.6163883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4625233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.9123.42573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51915297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.925158
X-RAY DIFFRACTIONr_chiral_restr0.0840.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021906
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02321
LS refinement shellResolution: 1.25→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 240 -
Rwork0.27 4797 -
all-5037 -
obs--93.14 %

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