2PC1 | pdb_00002pc1

Crystal structure of acetyltransferase GNAT family (NP_688560.1) from Streptococcus agalactiae 2603 at 1.28 A resolution

PDB DOI: https://doi.org/10.2210/pdb2PC1/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus agalactiae 2603V/R
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-03-29 Released: 2007-04-24
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free:
0.178 (Depositor), 0.190 (DCC)
R-Value Work:
0.167 (Depositor), 0.180 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of acetyltransferase GNAT family (NP_688560.1) from Streptococcus agalactiae 2603 at 1.28 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 23.97 kDa
Atom Count: 1,641
Modeled Residue Count: 173
Deposited Residue Count: 201
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyltransferase, GNAT family	A	201	Streptococcus agalactiae 2603V/R	Mutation(s): 5 Gene Names: NP_688560.1, SAG1567 EC: 2.3.1
UniProt
Find proteins for Q8DYC0 (Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R)) Explore Q8DYC0 Go to UniProtKB: Q8DYC0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DYC0
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

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: 1.28 Å
R-Value Free: 0.178 (Depositor), 0.190 (DCC)
R-Value Work: 0.167 (Depositor), 0.180 (DCC)
R-Value Observed: 0.167 (Depositor)

Diffraction Data: https://doi.org/10.18430/M32PC1

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.48	α = 94.22
b = 37.65	β = 109.42
c = 41.5	γ = 113.08

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
SHELXD	phasing
SOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-04-24

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-04-24
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2017-10-25
Changes: Author supporting evidence
Version 1.5: 2023-01-25
Changes: Database references, Derived calculations
Version 1.6: 2024-11-13
Changes: Data collection, Structure summary

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.