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- PDB-8ftn: E. coli ArnA dehydrogenase domain mutant - N492A -

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Basic information

Entry
Database: PDB / ID: 8ftn
TitleE. coli ArnA dehydrogenase domain mutant - N492A
ComponentsBifunctional UDP-4-amino-4-deoxy-L-arabinose formyltransferase/UDP-glucuronic acid oxidase ArnA
KeywordsOXIDOREDUCTASE / polymyxin resistance / UDP-glucuronic acid decarboxylase
Function / homology
Function and homology information


UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating) / UDP-4-amino-4-deoxy-L-arabinose formyltransferase / lipopolysaccharide biosynthetic process / carboxy-lyase activity / lipid A biosynthetic process / transferase activity / oxidoreductase activity / response to antibiotic
Similarity search - Function
Bifunctional polymyxin resistance protein ArnA-like, extended (e) SDRs / : / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Bifunctional UDP-4-amino-4-deoxy-L-arabinose formyltransferase/UDP-glucuronic acid oxidase ArnA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsSousa, M.C. / Mitchell, M.E.
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: Targeting the Conformational Change in ArnA Dehydrogenase for Selective Inhibition of Polymyxin Resistance.
Authors: Mitchell, M.E. / Gatzeva-Topalova, P.Z. / Bargmann, A.D. / Sammakia, T. / Sousa, M.C.
History
DepositionJan 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional UDP-4-amino-4-deoxy-L-arabinose formyltransferase/UDP-glucuronic acid oxidase ArnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4034
Polymers41,1151
Non-polymers2883
Water84747
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.129, 150.129, 150.129
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Space group name HallP4bd2ab3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+3/4,z+1/4,-y+1/4
#4: z+3/4,y+1/4,-x+1/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+3/4,x+1/4,-z+1/4
#20: -y+3/4,-x+3/4,-z+3/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+3/4,-y+3/4,-x+3/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+3/4,-z+3/4,-y+3/4
Components on special symmetry positions
IDModelComponents
11A-833-

HOH

21A-847-

HOH

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Components

#1: Protein Bifunctional UDP-4-amino-4-deoxy-L-arabinose formyltransferase/UDP-glucuronic acid oxidase ArnA


Mass: 41114.777 Da / Num. of mol.: 1 / Mutation: N492A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: arnA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8T5ZA36
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.43 Å3/Da / Density % sol: 64.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 3.2 M NaCl, 0.1 M bis Tris pH 5.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 13135 / % possible obs: 88.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 39.2 Å2 / Rpim(I) all: 0.059 / Net I/σ(I): 13.5
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2 / Num. unique obs: 410 / CC1/2: 0.755 / Rpim(I) all: 0.367 / Rrim(I) all: 0.62 / % possible all: 57.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.8→37.53 Å / SU ML: 0.3299 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.3087
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2656 644 4.99 %
Rwork0.2245 12253 -
obs0.2266 12897 87.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.77 Å2
Refinement stepCycle: LAST / Resolution: 2.8→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 15 47 2775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282791
X-RAY DIFFRACTIONf_angle_d0.55313779
X-RAY DIFFRACTIONf_chiral_restr0.0424406
X-RAY DIFFRACTIONf_plane_restr0.0149489
X-RAY DIFFRACTIONf_dihedral_angle_d4.9758367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.020.3281910.26731763X-RAY DIFFRACTION64.71
3.02-3.320.32771240.2622341X-RAY DIFFRACTION85.09
3.32-3.80.32731370.24042576X-RAY DIFFRACTION92.97
3.8-4.790.24721410.20152657X-RAY DIFFRACTION94.62
4.79-37.530.20971510.20852916X-RAY DIFFRACTION97.55

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