6FZ6 | pdb_00006fz6

Crystal Structure of a radical SAM methyltransferase from Sphaerobacter thermophilus

PDB DOI: https://doi.org/10.2210/pdb6FZ6/pdb

Classification: TRANSFERASE
Organism(s): Sphaerobacter thermophilus DSM 20745
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-03-14 Released: 2019-04-10
Deposition Author(s): Hinchliffe, P., Shaw, J.M., Spencer, J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free:
0.187 (Depositor), 0.191 (DCC)
R-Value Work:
0.166 (Depositor)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of a radical SAM methyltransferase from Sphaerobacter thermophilus

Shaw, J.M., Hinchliffe, P., Spencer, J.

To be published.

Macromolecule Content

Total Structure Weight: 83.12 kDa
Atom Count: 6,072
Modeled Residue Count: 682
Deposited Residue Count: 732
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable dual-specificity RNA methyltransferase RlmN	A, B	366	Sphaerobacter thermophilus DSM 20745	Mutation(s): 0 Gene Names: rlmN, Sthe_1821 EC: 2.1.1.192
UniProt
Find proteins for D1C4T7 (Sphaerobacter thermophilus (strain ATCC 49802 / DSM 20745 / KCCM 41009 / NCIMB 13125 / S 6022)) Explore D1C4T7 Go to UniProtKB: D1C4T7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D1C4T7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SMC Query on SMC	A, B	L-PEPTIDE LINKING	C₄ H₉ N O₂ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.187 (Depositor), 0.191 (DCC)
R-Value Work: 0.166 (Depositor)
R-Value Observed: 0.167 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.84	α = 90
b = 53.14	β = 90
c = 113.57	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
AutoSol	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-04-10

Deposition Author(s):

Hinchliffe, P.

Shaw, J.M.

Spencer, J.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/J017906/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M012107/1

Revision History (Full details and data files)

Version 1.0: 2019-04-10
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary