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- PDB-1yrw: Crystal Structure of E.coli ArnA Transformylase Domain -

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Basic information

Entry
Database: PDB / ID: 1yrw
TitleCrystal Structure of E.coli ArnA Transformylase Domain
Componentsprotein ArnA
KeywordsTRANSFERASE / Rossmann fold / OB-like fold
Function / homology
Function and homology information


UDP-4-deoxy-4-formamido-beta-L-arabinopyranose biosynthetic process / UDP-glucuronate 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 / UDP-D-xylose biosynthetic process / UDP-glucuronate decarboxylase activity / lipopolysaccharide biosynthetic process / lipid A biosynthetic process / NAD+ binding ...UDP-4-deoxy-4-formamido-beta-L-arabinopyranose biosynthetic process / UDP-glucuronate 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 / UDP-D-xylose biosynthetic process / UDP-glucuronate decarboxylase activity / lipopolysaccharide biosynthetic process / lipid A biosynthetic process / NAD+ binding / response to antibiotic / protein-containing complex / identical protein binding / membrane
Similarity search - Function
Bifunctional polymyxin resistance protein, ArnA / Formyl transferase, C-terminal domain / Bifunctional polymyxin resistance protein ArnA-like, extended (e) SDRs / 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 ...Bifunctional polymyxin resistance protein, ArnA / Formyl transferase, C-terminal domain / Bifunctional polymyxin resistance protein ArnA-like, extended (e) SDRs / 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
Bifunctional polymyxin resistance protein ArnA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGatzeva-Topalova, P.Z. / May, A.P. / Sousa, M.C.
CitationJournal: Biochemistry / Year: 2005
Title: Crystal structure and mechanism of the Escherichia coli ArnA (PmrI) transformylase domain. An enzyme for lipid A modification with 4-amino-4-deoxy-L-arabinose and polymyxin resistance.
Authors: Gatzeva-Topalova, P.Z. / May, A.P. / Sousa, M.C.
History
DepositionFeb 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protein ArnA


Theoretical massNumber of molelcules
Total (without water)32,8721
Polymers32,8721
Non-polymers00
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.103, 113.253, 124.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: Protein protein ArnA / Hypothetical protein yfbG


Mass: 32871.582 Da / Num. of mol.: 1 / Fragment: transformylase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YfbG / Plasmid: pMS195 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: P77398
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 12% PEG 6000, 0.5 M NaCl, 100 mM HEPES pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineTypeIDWavelengthWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONALS 5.0.321
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEMar 9, 2004
ADSC QUANTUM 42CCDJul 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
211
ReflectionResolution: 1.7→28.8 Å / Num. all: 46559 / Num. obs: 46093 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.025 / Net I/σ(I): 18.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 7.2 / Num. unique all: 4557 / % possible all: 98.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FMT

1fmt


Resolution: 1.7→28.76 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 496705.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4555 10.1 %RANDOM
Rwork0.198 ---
all0.1981 46476 --
obs0.1981 45262 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.4705 Å2 / ksol: 0.399819 e/Å3
Displacement parametersBiso mean: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2---2.52 Å20 Å2
3---2.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.7→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2213 0 0 274 2487
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.25 -9.4 %
Rwork0.215 3897 -
obs-4299 93.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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