3ONP

Crystal Structure of tRNA/rRNA Methyltransferase SpoU from Rhodobacter sphaeroides

PDB DOI: https://doi.org/10.2210/pdb3ONP/pdb

Classification: TRANSFERASE
Organism(s): Cereibacter sphaeroides 2.4.1
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2010-08-30 Released: 2010-09-08
Deposition Author(s): Kim, Y., Tesar, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.219
R-Value Work: 0.189
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of tRNA/rRNA Methyltransferase SpoU from Rhodobacter sphaeroides

Kim, Y., Tesar, C., Jedrzejczak, R., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 28.65 kDa
Atom Count: 1,486
Modelled Residue Count: 159
Deposited Residue Count: 249
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA/rRNA methyltransferase (SpoU)	A	249	Cereibacter sphaeroides 2.4.1	Mutation(s): 0 Gene Names: RHOS4_30450, RSP_3829 EC: 2.1.1.200
UniProt
Find proteins for Q3IXX1 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3IXX1 Go to UniProtKB: Q3IXX1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3IXX1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF 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]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain F [auth A] mmCIF format, chain C [auth A] mmCIF format, chain F [auth A]	C [auth A], F [auth A]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain F [auth A]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain G [auth A] MOL2 format, chain B [auth A] MOL2 format, chain G [auth A] mmCIF format, chain B [auth A] mmCIF format, chain G [auth A]	B [auth A], G [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain G [auth A] Interactions & Density Focus chain B [auth A] Focus chain G [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.219
R-Value Work: 0.189
R-Value Observed: 0.191
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.782	α = 90
b = 74.782	β = 90
c = 139.105	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
RESOLVE	model building
SOLVE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing