4KGN | pdb_00004kgn

Crystal structure of a tRNA (cytidine(34)-2'-O)-methyltransferase bound to S-adenosyl homocysteine

PDB DOI: https://doi.org/10.2210/pdb4KGN/pdb

Classification: TRANSFERASE
Organism(s): Burkholderia pseudomallei 1710b
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-04-29 Released: 2013-05-08
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.193 (Depositor), 0.192 (DCC)
R-Value Work:
0.169 (Depositor), 0.176 (DCC)
R-Value Observed:
0.170 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of a TrmH family tRNA methyltransferase bound to S-adenosyl homocysteine

Edwards, T.E., Fairman, J.W., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 143.94 kDa
Atom Count: 9,713
Modeled Residue Count: 1,220
Deposited Residue Count: 1,280
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (cytidine(34)-2'-O)-methyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H	160	Burkholderia pseudomallei 1710b	Mutation(s): 0 Gene Names: BURPS1710b_0668, trmL EC: 2.1.1.207
UniProt
Find proteins for Q3JWH1 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JWH1 Go to UniProtKB: Q3JWH1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3JWH1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth C] SDF format, chain Q [auth G] SDF format, chain N [auth E] MOL2 format, chain I [auth A] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth G] MOL2 format, chain N [auth E] mmCIF format, chain I [auth A] mmCIF format, chain L [auth C] mmCIF format, chain Q [auth G] mmCIF format, chain N [auth E]	I [auth A], L [auth C], N [auth E], Q [auth G]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain I [auth A] Focus chain L [auth C] Focus chain N [auth E] Focus chain Q [auth G] Interactions & Density Focus chain I [auth A] Focus chain L [auth C] Focus chain N [auth E] Focus chain Q [auth G]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain O [auth E] SDF format, chain P [auth F] SDF format, chain R [auth G] SDF format, chain K [auth B] SDF format, chain J [auth A] MOL2 format, chain M [auth C] MOL2 format, chain O [auth E] MOL2 format, chain P [auth F] MOL2 format, chain R [auth G] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] mmCIF format, chain M [auth C] mmCIF format, chain O [auth E] mmCIF format, chain P [auth F] mmCIF format, chain R [auth G] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A]	J [auth A] K [auth B] M [auth C] O [auth E] P [auth F] J [auth A], K [auth B], M [auth C], O [auth E], P [auth F], R [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth E] Focus chain P [auth F] Focus chain R [auth G] Interactions & Density Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth E] Focus chain P [auth F] Focus chain R [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.193 (Depositor), 0.192 (DCC)
R-Value Work: 0.169 (Depositor), 0.176 (DCC)
R-Value Observed: 0.170 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.6	α = 90
b = 149.71	β = 90.49
c = 80.3	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-05-08

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2013-05-08
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.