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- PDB-5j63: Crystal Structure of the N-terminal N-formyltransferase Domain (r... -

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Basic information

Entry
Database: PDB / ID: 5j63
TitleCrystal Structure of the N-terminal N-formyltransferase Domain (residues 1-306) of Escherichia coli Arna in Complex with UDP-Ara4N and Folinic Acid
ComponentsBifunctional polymyxin resistance protein ArnA
KeywordsTRANSFERASE / lipopolysaccharide
Function / homology
Function and homology information


UDP-glucuronic acid dehydrogenase activity / UDP-4-amino-4-deoxy-L-arabinose formyltransferase activity / UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating) / UDP-4-amino-4-deoxy-L-arabinose formyltransferase / lipopolysaccharide biosynthetic process / lipid A biosynthetic process / response to antibiotic
Similarity search - Function
Bifunctional polymyxin resistance protein, ArnA / Formyl transferase, C-terminal domain / Methionyl-tRNA Fmet Formyltransferase; Chain A, domain 2 / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal domain / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily ...Bifunctional polymyxin resistance protein, ArnA / Formyl transferase, C-terminal domain / Methionyl-tRNA Fmet Formyltransferase; Chain A, domain 2 / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal domain / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FNX / Chem-G3N / Bifunctional polymyxin resistance protein ArnA
Similarity search - Component
Biological speciesEscherichia coli H736 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsThoden, J.B. / Genthe, N.A. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115921 United States
CitationJournal: Protein Sci. / Year: 2016
Title: Structure of the Escherichia coli ArnA N-formyltransferase domain in complex with N(5) -formyltetrahydrofolate and UDP-Ara4N.
Authors: Genthe, N.A. / Thoden, J.B. / Holden, H.M.
History
DepositionApr 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Aug 10, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional polymyxin resistance protein ArnA
B: Bifunctional polymyxin resistance protein ArnA
C: Bifunctional polymyxin resistance protein ArnA
D: Bifunctional polymyxin resistance protein ArnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,50412
Polymers134,1134
Non-polymers3,3908
Water6,864381
1
A: Bifunctional polymyxin resistance protein ArnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3763
Polymers33,5281
Non-polymers8482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bifunctional polymyxin resistance protein ArnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3763
Polymers33,5281
Non-polymers8482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Bifunctional polymyxin resistance protein ArnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3763
Polymers33,5281
Non-polymers8482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Bifunctional polymyxin resistance protein ArnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3763
Polymers33,5281
Non-polymers8482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.994, 76.206, 84.852
Angle α, β, γ (deg.)89.94, 63.78, 61.54
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Bifunctional polymyxin resistance protein ArnA


Mass: 33528.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-terminal fragment of complete protein / Source: (gene. exp.) Escherichia coli H736 (bacteria) / Gene: arnA, ECHG_02161 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: F4SGI5
#2: Chemical
ChemComp-G3N / (2R,3R,4S,5S)-5-amino-3,4-dihydroxytetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate


Mass: 535.291 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H23N3O15P2
#3: Chemical
ChemComp-FNX / (4aS,6S)-2-amino-6-{(E)-[(4-methylphenyl)imino]methyl}-4-oxo-4,6,7,8-tetrahydropteridine-5(4aH)-carbaldehyde


Mass: 312.327 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H16N6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20 to 22% poly(ethylene glycol) 5000, 50 mM MgCl2, 5 mM N5-formyltetrahydrofolate, 10 mM UDP-Ara4N, and 100 mM HEPPS (pH 8.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.99768 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99768 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 45712 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 28.5
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 11.8 / % possible all: 88.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BLN

2bln


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.853 / SU B: 12.339 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R: 0.858 / ESU R Free: 0.354 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28404 2253 4.9 %RANDOM
Rwork0.21213 ---
obs0.21571 43477 91.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.422 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å2-1.35 Å21.28 Å2
2--1.31 Å20.18 Å2
3----2.11 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9145 0 228 381 9754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199710
X-RAY DIFFRACTIONr_bond_other_d0.0020.029233
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9713253
X-RAY DIFFRACTIONr_angle_other_deg0.991321171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2951206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60223.237414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.398151490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3561567
X-RAY DIFFRACTIONr_chiral_restr0.0880.21487
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110935
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022321
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1643.3864773
X-RAY DIFFRACTIONr_mcbond_other2.1633.3854772
X-RAY DIFFRACTIONr_mcangle_it3.4745.0675957
X-RAY DIFFRACTIONr_mcangle_other3.4745.0675958
X-RAY DIFFRACTIONr_scbond_it2.0693.5464937
X-RAY DIFFRACTIONr_scbond_other2.0693.5464936
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4355.2397284
X-RAY DIFFRACTIONr_long_range_B_refined5.52526.26110802
X-RAY DIFFRACTIONr_long_range_B_other5.49326.29110704
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 143 -
Rwork0.268 3087 -
obs--88.64 %

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