5KZK | pdb_00005kzk

Crystal Structure of rRNA methyltransferase from Sinorhizobium meliloti

• PDB DOI: https://doi.org/10.2210/pdb5KZK/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-07-25 Released: 2017-08-02 
• Deposition Author(s): Dey, D., Hegde, R.P., Almo, S.C., Ramakumar, S., Ramagopal, U.A., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.259 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Crystal Structure of rRNA methyltransferase from Sinorhizobium meliloti

Dey, D., Hegde, R.P., Almo, S.C., Ramakumar, S., Ramagopal, U.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.44 kDa 
• Atom Count: 3,980 
• Modeled Residue Count: 521 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable RNA methyltransferase, TrmH family	A, B	288	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: SMc01130 EC: 2.1.1
UniProt
Find proteins for Q92SJ4 (Rhizobium meliloti (strain 1021)) Explore Q92SJ4  Go to UniProtKB:  Q92SJ4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CO	C [auth A], E [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.259 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.82	α = 90
b = 84.302	β = 90
c = 112.045	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data processing
SHELXDE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-02 
Deposition Author(s): Dey, D., Hegde, R.P., Almo, S.C., Ramakumar, S., Ramagopal, U.A., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2017-08-02
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Derived calculations
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary