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- PDB-7txp: X-ray structure of the VioB N-acetyltransferase from Acinetobacte... -

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Basic information

Entry
Database: PDB / ID: 7txp
TitleX-ray structure of the VioB N-acetyltransferase from Acinetobacter baumannii in complex with TDP-4-amino-4,6-dideoxy-D-glucose
ComponentsVioB
KeywordsTRANSFERASE / N-acetyltransferase / beta helix / 4-amino-4 / 6-dideoxy-D-glucose
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
dTDP-4-amino-4,6-dideoxyglucose / VioB
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 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)23,8994
Polymers23,3061
Non-polymers5933
Water3,801211
1
A: VioB
hetero molecules

A: VioB
hetero molecules

A: VioB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,69812
Polymers69,9183
Non-polymers1,7809
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 area5690 Å2
ΔGint-41 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.001, 97.001, 73.285
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-547-

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-0FX / dTDP-4-amino-4,6-dideoxyglucose


Mass: 547.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H27N3O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 211 / 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: 56.8 %
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). Soak in ligand fre solution followed by soak in 20 mM dTDP-4- ...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). Soak in ligand fre solution followed by soak in 20 mM dTDP-4-amino-4,6-dideoxy-D-glucose

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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 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 45094 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.069 / Net I/σ(I): 10.4
Reflection shellResolution: 1.45→1.55 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3 / Num. unique obs: 8089 / Rsym value: 0.353 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
SADABSdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4m98

4m98


Resolution: 1.45→36.47 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.117 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2240 5 %RANDOM
Rwork0.1766 ---
obs0.1774 42854 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.03 Å2 / Biso mean: 12.155 Å2 / Biso min: 4.53 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.45→36.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 37 211 1804
Biso mean--11.12 23.83 -
Num. residues----209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131656
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171614
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.6292261
X-RAY DIFFRACTIONr_angle_other_deg1.4091.5723746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8155222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.29723.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73315289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.249158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021829
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02311
LS refinement shellResolution: 1.45→1.487 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.231 175 -
Rwork0.234 3072 -
obs--95.22 %

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