9IAF | pdb_00009iaf

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

PDB DOI: https://doi.org/10.2210/pdb9IAF/pdb

Classification: TRANSFERASE
Organism(s): Mycolicibacterium smegmatis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-02-10 Released: 2025-12-17
Deposition Author(s): Alaviuhkola, J., Abdulmajeed, S., Lehtio, L.
Funding Organization(s): Sigrid Juselius Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.250 (Depositor), 0.215 (DCC)
R-Value Work:
0.187 (Depositor), 0.199 (DCC)

Starting Model: experimental
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Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 17.04 kDa
Atom Count: 1,209
Modeled Residue Count: 140
Deposited Residue Count: 143
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rifampin ADP-ribosyl transferase	A	143	Mycolicibacterium smegmatis	Mutation(s): 2 Gene Names: BIN_B_03083
UniProt
Find proteins for A0A653FGA6 (Mycolicibacterium smegmatis) Explore A0A653FGA6 Go to UniProtKB: A0A653FGA6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A653FGA6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RFP Query on RFP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	RIFAMPICIN C₄₃ H₅₈ N₄ O₁₂ JQXXHWHPUNPDRT-WLSIYKJHSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
A1I1V (Subject of Investigation/LOI) Query on A1I1V Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-amino-6-chloro-3-phenyl-1H-quinolin-4-one C₁₅ H₁₁ Cl N₂ O BQEKTAOKRNWDNE-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.250 (Depositor), 0.215 (DCC)
R-Value Work: 0.187 (Depositor), 0.199 (DCC)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.22	α = 90
b = 60.76	β = 93.485
c = 45.55	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-17

Deposition Author(s):

Alaviuhkola, J.

Abdulmajeed, S.

Funding Organization	Location	Grant Number
Sigrid Juselius Foundation	Finland	--

Revision History (Full details and data files)

Version 1.0: 2025-12-17
Type: Initial release

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