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- PDB-1z7e: Crystal structure of full length ArnA -

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Basic information

Entry
Database: PDB / ID: 1z7e
TitleCrystal structure of full length ArnA
Componentsprotein ArnA
KeywordsHYDROLASE / 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
Rossmann fold - #12230 / Bifunctional polymyxin resistance protein, ArnA / 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 / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily ...Rossmann fold - #12230 / Bifunctional polymyxin resistance protein, ArnA / 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 / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / Bifunctional polymyxin resistance protein ArnA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGatzeva-Topalova, P.Z. / May, A.P. / Sousa, M.C.
CitationJournal: Structure / Year: 2005
Title: Structure and Mechanism of ArnA: Conformational Change Implies Ordered Dehydrogenase Mechanism in Key Enzyme for Polymyxin Resistance
Authors: Gatzeva-Topalova, P.Z. / May, A.P. / Sousa, M.C.
History
DepositionMar 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protein ArnA
B: protein ArnA
C: protein ArnA
D: protein ArnA
E: protein ArnA
F: protein ArnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)452,83918
Polymers446,3156
Non-polymers6,52512
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33970 Å2
ΔGint-146 kcal/mol
Surface area145130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.689, 166.227, 261.992
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein
protein ArnA / Hypothetical protein yfbG


Mass: 74385.773 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: full length / Source: (gene. exp.) Escherichia coli (E. coli) / Description: plasmid is AN ENGINEERED VARIANT OF THE PET28 / Gene: PMRI, YFBG / Plasmid: PMS122 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA (DE3) / References: UniProt: P77398
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-UGA / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-GLUCURONIC ACID


Mass: 580.285 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H22N2O18P2

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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: 3.7 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M MES pH 7.0, 10% Ethylene glycol, 9% PEG 8000, 14 mM 2mercaptoethanol and 10 mM ATP; protein was pre-incubated on ice with 3mM UDP-GlcA and 3 mM MgSO4 , VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1808 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2003
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 132644 / Num. obs: 131520 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.3 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3.9 / Num. unique all: 13215 / % possible all: 99.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U9J, 1YRW

1u9j

1yrw


Resolution: 3→50 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 135954.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 12667 10 %RANDOM
Rwork0.225 ---
all0.2251 132762 --
obs0.2251 126417 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.7321 Å2 / ksol: 0.390853 e/Å3
Displacement parametersBiso mean: 44.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å20 Å20 Å2
2---12.76 Å20 Å2
3---14.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30148 0 408 0 30556
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it0.971.5
X-RAY DIFFRACTIONc_mcangle_it1.692
X-RAY DIFFRACTIONc_scbond_it1.612
X-RAY DIFFRACTIONc_scangle_it2.632.5
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.334 1169 9.9 %
Rwork0.317 10626 -
obs-11795 89.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMATP_UGA_REV.TOP
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4ATP_UGA_REV.PARAM

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