5CO4

Structural insights into the 2-OH methylation of C/U34 on tRNA

PDB DOI: https://doi.org/10.2210/pdb5CO4/pdb

Classification: TRANSFERASE
Organism(s): Thermus thermophilus HB27
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-07-19 Released: 2016-07-20
Deposition Author(s): Xie, W., Pang, P., Wang, Z.
Funding Organization(s): Guangdong Innovative Research Team Program

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.200
R-Value Work: 0.173
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural insights into the 2-OH methylation of C34 or U34 on tRNA

Xie, W., Pang, P., Wang, Z.

To be published.

Macromolecule Content

Total Structure Weight: 40.8 kDa
Atom Count: 2,790
Modelled Residue Count: 313
Deposited Residue Count: 356
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative tRNA (cytidine(34)-2'-O)-methyltransferase	A [auth B], B [auth A]	178	Thermus thermophilus HB27	Mutation(s): 0 Gene Names: TT_C1952 EC: 2.1.1.207
UniProt
Find proteins for Q72G96 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72G96 Go to UniProtKB: Q72G96
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q72G96
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MTA Query on MTA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain C [auth B] MOL2 format, chain E [auth A] MOL2 format, chain C [auth B]	C [auth B], E [auth A]	5'-DEOXY-5'-METHYLTHIOADENOSINE C₁₁ H₁₅ N₅ O₃ S WUUGFSXJNOTRMR-IOSLPCCCSA-N		Interactions Focus chain C [auth B] Focus chain E [auth A] Interactions & Density Focus chain C [auth B] Focus chain E [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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: 1.70 Å
R-Value Free: 0.200
R-Value Work: 0.173
R-Value Observed: 0.174
Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.296	α = 90
b = 95.296	β = 90
c = 61.599	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-07-20

Deposition Author(s):

Xie, W.

Pang, P.

Wang, Z.

Funding Organization	Location	Grant Number
Guangdong Innovative Research Team Program	China	2011Y038

Revision History (Full details and data files)

Version 1.0: 2016-07-20
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

5CO4

Structural insights into the 2-OH methylation of C/U34 on tRNA

Structural insights into the 2-OH methylation of C34 or U34 on tRNA

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)