4X3L | pdb_00004x3l

Crystal Structure of TTHA0275 from Thermus thermophilus (HB8) in complex with 5'-methylthioadenosine in space group P21212

• PDB DOI: https://doi.org/10.2210/pdb4X3L/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-01 Released: 2016-01-20 
• Deposition Author(s): Demirci, H., Belardinelli, R., Jogl, G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.207 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of TTHA0275 from Thermus thermophilus (HB8)

Demirci, H., Belardinelli, R., Jogl, G.

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: 56.84 kDa 
• Atom Count: 4,521 
• Modeled Residue Count: 520 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA 2'-O ribose methyltransferase	A, B	260	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA0275
UniProt
Find proteins for Q5SLL8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLL8  Go to UniProtKB:  Q5SLL8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTA	C [auth A], F [auth B]	5'-DEOXY-5'-METHYLTHIOADENOSINE C11 H15 N5 O3 S WUUGFSXJNOTRMR-IOSLPCCCSA-N
CL	D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.207 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.17	α = 90
b = 115.95	β = 90
c = 58.68	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Demirci, H., Belardinelli, R., Jogl, G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM019756
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094157

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2017-03-22
  Changes: Source and taxonomy
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description