2FIW | pdb_00002fiw

Crystal Structure of the GCN5-Related N-acetyltransferase: Aminotransferase, Class-II from Rhodopseudomonas palustris

PDB DOI: https://doi.org/10.2210/pdb2FIW/pdb

Classification: TRANSFERASE
Organism(s): Rhodopseudomonas palustris CGA009
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2005-12-30 Released: 2006-02-14
Deposition Author(s): Kim, Y., Skarina, T., Onopriyenko, O., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.263 (Depositor), 0.261 (DCC)
R-Value Work:
0.219 (Depositor), 0.218 (DCC)
R-Value Observed:
0.223 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of the GCN5-Related N-acetyltransferase: Aminotransferase, Class-II from Rhodopseudomonas palustris

Kim, Y., Skarina, T., Onopriyenko, O., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 19.17 kDa
Atom Count: 1,403
Modeled Residue Count: 160
Deposited Residue Count: 172
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GCN5-related N-acetyltransferase:Aminotransferase, class-II	A	172	Rhodopseudomonas palustris CGA009	Mutation(s): 4
UniProt
Find proteins for Q6N8A5 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N8A5 Go to UniProtKB: Q6N8A5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6N8A5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO Query on ACO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		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: 2.35 Å
R-Value Free: 0.263 (Depositor), 0.261 (DCC)
R-Value Work: 0.219 (Depositor), 0.218 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.293	α = 90
b = 78.293	β = 90
c = 93.242	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
MLPHARE	phasing
RESOLVE	phasing
SHELXE	model building
SHELXD	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-02-14

Deposition Author(s):

Onopriyenko, O.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2006-02-14
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2024-12-25
Changes: Advisory, Data collection, Database references, Derived calculations, 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.