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- PDB-8t0j: Salmonella Typhimurium ArnD -

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Basic information

Entry
Database: PDB / ID: 8t0j
TitleSalmonella Typhimurium ArnD
ComponentsProbable 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD
KeywordsHYDROLASE / polymyxin resistance / undecaprenyl-phospho-4-deoxy-4-formamido-arabinose deformylase / carbohydrate esterase
Function / homology
Function and homology information


: / 4-amino-4-deoxy-alpha-L-arabinopyranosyl undecaprenyl phosphate biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / lipopolysaccharide biosynthetic process / lipid A biosynthetic process / response to antibiotic
Similarity search - Function
4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD, probable / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel
Similarity search - Domain/homology
Probable 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsSousa, M.C. / Munoz-Escudero, D. / Lee, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)2R56AI060841 United States
CitationJournal: Biochemistry / Year: 2023
Title: Structure and Function of ArnD. A Deformylase Essential for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance.
Authors: Munoz-Escudero, D. / Breazeale, S.D. / Lee, M. / Guan, Z. / Raetz, C.R.H. / Sousa, M.C.
History
DepositionJun 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD


Theoretical massNumber of molelcules
Total (without water)32,9521
Polymers32,9521
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.551, 85.646, 111.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Probable 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD


Mass: 32951.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: arnD, pbgP4, pmrJ, STM2300 / Production host: Escherichia coli (E. coli)
References: UniProt: O52326, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3 Å3/Da / Density % sol: 59.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: Crystals of ArnD were obtained by mixing 2 uL of a stock solution of ArnD (6 mg/mL) in 25mM Tris-HCl, pH8.0, 150mM NaCl, 10% glycerol, 5mM BME, 0.0174% DDM, with 2 uL of a precipitant ...Details: Crystals of ArnD were obtained by mixing 2 uL of a stock solution of ArnD (6 mg/mL) in 25mM Tris-HCl, pH8.0, 150mM NaCl, 10% glycerol, 5mM BME, 0.0174% DDM, with 2 uL of a precipitant solution containing 0.1M Na citrate pH 6.2, 10% isopropanol and 17% PEG4000 and allowing vapor diffusion between the protein droplet and a 1mL reservoir of precipitant in a hanging drop set up incubated at 16 degrees Celsius.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.59→40.74 Å / Num. obs: 11633 / % possible obs: 91.44 % / Redundancy: 2.7 % / Biso Wilson estimate: 36.33 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.0816 / Rpim(I) all: 0.05888 / Rrim(I) all: 0.1012 / Net I/σ(I): 12.82
Reflection shellResolution: 2.59→2.683 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.2342 / Mean I/σ(I) obs: 3.99 / Num. unique obs: 861 / CC1/2: 0.939 / CC star: 0.984 / Rpim(I) all: 0.1725 / Rrim(I) all: 0.2924 / % possible all: 70.43

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→40.74 Å / SU ML: 0.3021 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.7539
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2873 578 4.99 %
Rwork0.2254 11009 -
obs0.2284 11587 91.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.01 Å2
Refinement stepCycle: LAST / Resolution: 2.59→40.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 0 10 2094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742136
X-RAY DIFFRACTIONf_angle_d0.97032907
X-RAY DIFFRACTIONf_chiral_restr0.0502322
X-RAY DIFFRACTIONf_plane_restr0.0088378
X-RAY DIFFRACTIONf_dihedral_angle_d17.4098765
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.850.31451210.26062223X-RAY DIFFRACTION75.39
2.85-3.260.33961590.26732817X-RAY DIFFRACTION94.93
3.26-4.110.2861570.21042969X-RAY DIFFRACTION98.89
4.11-40.740.2541410.21083000X-RAY DIFFRACTION95.65

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