PDB-9iaf: Crystal structure of Arr in complex with Rifampicin and Chr-16

ID or keywords:

Entry

Database: PDB / ID: 9iaf

Title

Crystal structure of Arr in complex with Rifampicin and Chr-16

Components

Rifampin ADP-ribosyl transferase

Keywords

TRANSFERASE / ADP-ribosyltransferase / complex / inhibitor / rifampicin

Function / homology

Rifampin ADP-ribosyltransferase / Rifampin ADP-ribosyltransferase superfamily / Rifampin ADP-ribosyl transferase / transferase activity / : / RIFAMPICIN / Rifampin ADP-ribosyl transferase

Function and homology information

Biological species

Mycolicibacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Alaviuhkola, J. / Abdulmajeed, S. / Lehtio, L.

Funding support

Finland, 1items

Citation

Journal: To Be Published
Title: Crystal structure of Arr in complex with Rifampicin and Chr-16
Authors: Alaviuhkola, J. / Abdulmajeed, S. / Lehtio, L.

History

Deposition	Feb 10, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 17, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9iaf.cif.gz	48.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9iaf.ent.gz		Display	PDB format
PDBx/mmJSON format	9iaf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ia/9iaf ftp://data.pdbj.org/pub/pdb/validation_reports/ia/9iaf	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.23729/a14040e9-f046-42c5-b7ab-7d9c53dc0bae Data set type: diffraction image data Metadata reference: 10.23729/a14040e9-f046-42c5-b7ab-7d9c53dc0bae

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Rifampin ADP-ribosyl transferase

hetero molecules

17 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	56.220, 60.760, 45.550
Angle α, β, γ (deg.)	90.000, 93.485, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Rifampin ADP-ribosyl transferase Mass: 15863.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: BIN_B_03083 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A653FGA6
#2: Chemical	ChemComp-A1I1V / 2-amino-6-chloro-3-phenyl-1H-quinolin-4-one / 2-azanyl-6-chloranyl-3-phenyl-1H-quinolin-4-one Mass: 270.714 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₅H₁₁ClN₂O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-RFP / RIFAMPICIN Mass: 822.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄₃H₅₈N₄O₁₂ / Comment: antibiotic*YM
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.74 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 10 mg/ml protein, 1 mM rifampicin, 1 mM inhibitor (Chr-16), 50 mM Tris pH 8.2, 0.2 M MgCl2, 10% (w/v) PEG 8000, 20% (v/v) 2-methyl-2,4-pentanediol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.953745 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 23, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.953745 Å / Relative weight: 1
Reflection	Resolution: 2.2→45.466 Å / Num. obs: 7819 / % possible obs: 99.4 % / Redundancy: 10.99 % / CC_1/2: 0.999 / Net I/σ(I): 12.53
Reflection shell	Resolution: 2.2→2.26 Å / Redundancy: 6.69 % / Mean I/σ(I) obs: 1.87 / Num. unique obs: 569 / CC_1/2: 0.797 / % possible all: 96.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→45.466 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.934 / SU B: 7.234 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.229
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2503	506	6.471 %	Random selection
R_work	0.187	7313	-	-
all	0.191	-	-	-
obs	-	7819	99.428 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 46.161 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.807 Å²	0 Å²	-0.046 Å²
2-	-	-2.545 Å²	-0 Å²
3-	-	-	-0.255 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→45.466 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1099	0	82	28	1209

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	1213
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1131
X-RAY DIFFRACTION	r_angle_refined_deg	1.865	1.668	1657
X-RAY DIFFRACTION	r_angle_other_deg	1.335	1.58	2597
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.939	5	139
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.358	20.278	72
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.949	15	183
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.733	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	149
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	1378
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	274
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	222
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	1110
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	585
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	588
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.127	0.2	44
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.134	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.249	0.2	50
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.178	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	4.981	4.583	559
X-RAY DIFFRACTION	r_mcbond_other	4.978	4.582	558
X-RAY DIFFRACTION	r_mcangle_it	6.949	6.851	697
X-RAY DIFFRACTION	r_mcangle_other	6.945	6.851	698
X-RAY DIFFRACTION	r_scbond_it	5.91	5.1	654
X-RAY DIFFRACTION	r_scbond_other	5.905	5.101	655
X-RAY DIFFRACTION	r_scangle_it	8.077	7.476	960
X-RAY DIFFRACTION	r_scangle_other	8.073	7.478	961
X-RAY DIFFRACTION	r_lrange_it	10.665	52.623	1382
X-RAY DIFFRACTION	r_lrange_other	10.661	52.624	1382

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.2-2.257	0.482	32	0.437	536	0.439	590	0.568	0.636	96.2712	0.444
2.257-2.319	0.519	38	0.341	508	0.353	558	0.636	0.724	97.8495	0.355
2.319-2.386	0.319	45	0.226	495	0.234	541	0.801	0.842	99.8152	0.202
2.386-2.459	0.327	43	0.223	486	0.231	530	0.825	0.864	99.8113	0.2
2.459-2.539	0.323	44	0.175	466	0.184	510	0.782	0.923	100	0.151
2.539-2.628	0.307	33	0.176	471	0.184	504	0.864	0.925	100	0.15
2.628-2.727	0.212	34	0.164	451	0.167	487	0.928	0.94	99.5893	0.14
2.727-2.838	0.25	19	0.159	436	0.163	456	0.902	0.944	99.7807	0.133
2.838-2.963	0.225	25	0.153	427	0.158	453	0.934	0.945	99.7793	0.133
2.963-3.107	0.298	20	0.152	396	0.157	417	0.877	0.946	99.7602	0.135
3.107-3.275	0.218	23	0.155	379	0.159	402	0.94	0.947	100	0.141
3.275-3.472	0.221	16	0.162	367	0.164	383	0.916	0.95	100	0.149
3.472-3.71	0.211	34	0.156	331	0.16	368	0.936	0.956	99.1848	0.144
3.71-4.005	0.251	16	0.146	317	0.151	334	0.943	0.961	99.7006	0.14
4.005-4.384	0.174	22	0.156	284	0.157	306	0.96	0.962	100	0.157
4.384-4.896	0.251	21	0.16	261	0.166	282	0.94	0.963	100	0.168
4.896-5.643	0.246	14	0.209	242	0.211	256	0.903	0.954	100	0.228
5.643-6.884	0.22	15	0.241	208	0.239	223	0.939	0.935	100	0.25
6.884-9.626	0.205	8	0.211	152	0.21	160	0.968	0.949	100	0.232
9.626-45.466	0.256	4	0.24	100	0.241	104	0.937	0.919	100	0.251

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