6AIE | pdb_00006aie

Crystal structure of a new form of RsmD-like RNA methyl transferase from Mycobacterium tuberculosis determined at 1.74 A resolution

PDB DOI: https://doi.org/10.2210/pdb6AIE/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-08-22 Released: 2018-09-26
Deposition Author(s): Venkataraman, S., Dhankar, A., Sinha, K.M., Manivasakan, P., Iqbal, N., Singh, T.P., Prasad, B.V.L.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.243 (Depositor), 0.253 (DCC)
R-Value Work:
0.211 (Depositor), 0.222 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a new form of RsmD-like RNA methyl transferase from Mycobacterium tuberculosis determined at 1.74 A resolution

Venkataraman, S., Dhankar, A., Sinha, K.M., Bandopadhyay, K., Iqbal, N., Singh, T.P., Prasad, V.L.S.B.

To be published.

Macromolecule Content

Total Structure Weight: 59.74 kDa
Atom Count: 4,354
Modeled Residue Count: 546
Deposited Residue Count: 567
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative methyltransferase	A, B, C	189	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: rsmD, ERS007661_01921, ERS007663_00818, ERS007665_01852, ERS007672_04225, ERS007681_00248, ERS007722_02698, ERS007739_01109, ERS007741_03599, ERS023446_00051... rsmD, ERS007661_01921, ERS007663_00818, ERS007665_01852, ERS007672_04225, ERS007681_00248, ERS007722_02698, ERS007739_01109, ERS007741_03599, ERS023446_00051, ERS027646_01755, ERS027651_01374, ERS027652_01710, ERS027654_02036, ERS027656_00358, ERS027659_03553, ERS031537_04978, SAMEA2682864_00651, SAMEA2683035_02297 EC: 2.1.1.171 (PDB Primary Data), 2.1.1 (UniProt)
UniProt
Find proteins for I6XFS7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6XFS7 Go to UniProtKB: I6XFS7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I6XFS7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.243 (Depositor), 0.253 (DCC)
R-Value Work: 0.211 (Depositor), 0.222 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.782	α = 90
b = 55.3	β = 90
c = 100.74	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-09-26

Deposition Author(s):

Venkataraman, S.

Manivasakan, P.

Prasad, B.V.L.S.

Revision History (Full details and data files)

Version 1.0: 2018-09-26
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.