3NTV | pdb_00003ntv

Crystal structure of a putative caffeoyl-CoA O-methyltransferase from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb3NTV/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus subsp. aureus MW2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-07-05 Released: 2011-07-06
Deposition Author(s): Qiu, W., Lam, R., Romanov, V., Jones, K., Pai, E.F., Chirgadze, N.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.205 (Depositor), 0.210 (DCC)
R-Value Work:
0.176 (Depositor), 0.181 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3NTV

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a putative caffeoyl-CoA O-methyltransferase from Staphylococcus aureus

Qiu, W., Lam, R., Romanov, V., Jones, K., Pai, E.F., Chirgadze, N.Y.

To be published.

Macromolecule Content

Total Structure Weight: 54.3 kDa
Atom Count: 3,838
Modeled Residue Count: 420
Deposited Residue Count: 464
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MW1564 protein	A, B	232	Staphylococcus aureus subsp. aureus MW2	Mutation(s): 0 Gene Names: MW1564 EC: 2.1.1.104

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.205 (Depositor), 0.210 (DCC)
R-Value Work: 0.176 (Depositor), 0.181 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.383	α = 90
b = 65.441	β = 90.9
c = 70.468	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SHARP	phasing
BUSTER	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-07-06

Deposition Author(s):

Chirgadze, N.Y.

Revision History (Full details and data files)

Version 1.0: 2011-07-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.3: 2024-10-09
Changes: Structure summary

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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.