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- PDB-9iba: Crystal structure of Arr-2 in complex with Rifampicin -

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Basic information

Entry
Database: PDB / ID: 9iba
TitleCrystal structure of Arr-2 in complex with Rifampicin
ComponentsARR-2
KeywordsTRANSFERASE / Arr / rifampicin / ADP-ribosyltransferase
Function / homologyRifampin ADP-ribosyltransferase / Rifampin ADP-ribosyltransferase superfamily / Rifampin ADP-ribosyl transferase / transferase activity / RIFAMPICIN / ARR-2
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsAlaviuhkola, J. / Abdulmajeed, S. / Lehtio, L.
Funding support Finland, 1items
OrganizationGrant numberCountry
Sigrid Juselius Foundation Finland
CitationJournal: To Be Published
Title: Crystal structure of Arr-2 in complex with Rifampicin
Authors: Alaviuhkola, J. / Abdulmajeed, S. / Lehtio, L.
History
DepositionFeb 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARR-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6933
Polymers17,0471
Non-polymers1,6462
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-15 kcal/mol
Surface area8410 Å2
Unit cell
Length a, b, c (Å)41.260, 42.970, 85.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ARR-2 / Arr2 / Rifampin ADP-ribosylating transferase


Mass: 17047.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: arr-2, arr2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O87490
#2: Chemical ChemComp-RFP / RIFAMPICIN


Mass: 822.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C43H58N4O12 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5 mg/ml, 1 mM inhibitor (7-chloro-2-{4-[(2-hydroxyethyl)(methyl)amino]phenyl}-3,4-dihydroquinazolin-4-one), 1 mM rifampicin, 100 mM MOPS pH 7.5, 20% ethanol, and 2.7 M (NH4)2 SO4.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 30653 / % possible obs: 99.6 % / Redundancy: 5.01 % / CC1/2: 0.998 / Net I/σ(I): 12.41
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 5.12 % / Mean I/σ(I) obs: 2.12 / Num. unique obs: 2251 / CC1/2: 0.784 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→38.423 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.5 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.058
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1846 1531 5.003 %
Rwork0.1431 29071 -
all0.145 --
obs-30602 99.639 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.266 Å2-0 Å2-0 Å2
2---0.193 Å20 Å2
3---0.459 Å2
Refinement stepCycle: LAST / Resolution: 1.4→38.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 0 118 115 1388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131330
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151221
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.6671828
X-RAY DIFFRACTIONr_angle_other_deg1.3671.5732819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0595150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.93120.39576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25715198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.798157
X-RAY DIFFRACTIONr_chiral_restr0.0810.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021492
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02286
X-RAY DIFFRACTIONr_nbd_refined0.210.2238
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.21188
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2654
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2599
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.295
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2250.28
X-RAY DIFFRACTIONr_nbd_other0.2150.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1240.215
X-RAY DIFFRACTIONr_mcbond_it2.781.953585
X-RAY DIFFRACTIONr_mcbond_other2.6581.948584
X-RAY DIFFRACTIONr_mcangle_it3.5022.952731
X-RAY DIFFRACTIONr_mcangle_other3.5132.956732
X-RAY DIFFRACTIONr_scbond_it4.3492.4745
X-RAY DIFFRACTIONr_scbond_other4.3392.393743
X-RAY DIFFRACTIONr_scangle_it5.1093.4571094
X-RAY DIFFRACTIONr_scangle_other5.1133.4561094
X-RAY DIFFRACTIONr_lrange_it5.71724.4771571
X-RAY DIFFRACTIONr_lrange_other5.5924.1981549
X-RAY DIFFRACTIONr_rigid_bond_restr2.70632551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4360.2341120.2172130X-RAY DIFFRACTION99.5118
1.436-1.4760.2341090.1962062X-RAY DIFFRACTION99.7244
1.476-1.5180.2641050.1742001X-RAY DIFFRACTION99.8104
1.518-1.5650.2251030.1581954X-RAY DIFFRACTION99.9029
1.565-1.6160.1821000.1351895X-RAY DIFFRACTION99.75
1.616-1.6730.2960.1271823X-RAY DIFFRACTION99.6883
1.673-1.7360.191940.1271790X-RAY DIFFRACTION99.841
1.736-1.8070.171900.1091713X-RAY DIFFRACTION99.9446
1.807-1.8870.186870.1111644X-RAY DIFFRACTION99.827
1.887-1.980.151830.1171582X-RAY DIFFRACTION99.8201
1.98-2.0870.228790.1331483X-RAY DIFFRACTION99.3639
2.087-2.2130.145750.1111425X-RAY DIFFRACTION99.2063
2.213-2.3660.19700.1161324X-RAY DIFFRACTION99.7853
2.366-2.5550.166660.1321264X-RAY DIFFRACTION99.9249
2.555-2.7990.222610.151160X-RAY DIFFRACTION99.511
2.799-3.1290.134570.1411063X-RAY DIFFRACTION99.8217
3.129-3.6120.162490.143929X-RAY DIFFRACTION99.0881
3.612-4.4220.194410.143807X-RAY DIFFRACTION99.0654
4.422-6.2450.184340.173640X-RAY DIFFRACTION99.1176
6.245-38.4230.211200.225382X-RAY DIFFRACTION97.5728

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