4ISC

Crystal structure of a putative Methyltransferase from Pseudomonas syringae

PDB DOI: https://doi.org/10.2210/pdb4ISC/pdb

Classification: TRANSFERASE
Organism(s): Pseudomonas syringae pv. tomato str. DC3000
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-01-16 Released: 2013-02-20
Deposition Author(s): Filippova, E.V., Wawrzak, Z., Minasov, G., Shuvalova, L., Kiryukhina, O., Clancy, S., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free: 0.277
R-Value Work: 0.190
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of a putative Methyltransferase from Pseudomonas syringae

Filippova, E.V., Wawrzak, Z., Minasov, G., Shuvalova, L., Kiryukhina, O., Clancy, S., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 18.9 kDa
Atom Count: 1,290
Modelled Residue Count: 156
Deposited Residue Count: 164
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase	A	164	Pseudomonas syringae pv. tomato str. DC3000	Mutation(s): 0
UniProt
Find proteins for Q880M1 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q880M1 Go to UniProtKB: Q880M1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q880M1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [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: 2.78 Å
R-Value Free: 0.277
R-Value Work: 0.190
R-Value Observed: 0.194
Space Group: P 4₃ 2₁ 2
Diffraction Data: https://doi.org/10.18430/M34ISC

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.46	α = 90
b = 43.46	β = 90
c = 181.29	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-02-20

Deposition Author(s):

Filippova, E.V.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-02-20
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2018-01-24
Changes: Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.