4H89 | pdb_00004h89

The Structure of a GCN5-Related N-Acetyltransferase from Kribbella flavida

PDB DOI: https://doi.org/10.2210/pdb4H89/pdb

Classification: TRANSFERASE
Organism(s): Kribbella flavida DSM 17836
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-09-21 Released: 2012-10-10
Deposition Author(s): Cuff, M.E., Mcknight, S.M., Mack, J.C., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.37 Å
R-Value Free:
0.159 (Depositor), 0.160 (DCC)
R-Value Work:
0.117 (Depositor), 0.118 (DCC)
R-Value Observed:
0.120 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The Structure of a GCN5-Related N-Acetyltransferase from Kribbella flavida.

Cuff, M.E., Mcknight, S.M., Mack, J.C., Endres, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 18.96 kDa
Atom Count: 1,676
Modeled Residue Count: 168
Deposited Residue Count: 173
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GCN5-related N-acetyltransferase	A	173	Kribbella flavida DSM 17836	Mutation(s): 0 Gene Names: Kfla_6915
UniProt
Find proteins for D2Q3N2 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)) Explore D2Q3N2 Go to UniProtKB: D2Q3N2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D2Q3N2
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 1.37 Å
R-Value Free: 0.159 (Depositor), 0.160 (DCC)
R-Value Work: 0.117 (Depositor), 0.118 (DCC)
R-Value Observed: 0.120 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.482	α = 90
b = 64.913	β = 100.68
c = 56.569	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-10-10

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2012-10-10
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, 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.