6WQB | pdb_00006wqb

Crystal structure of VipF from Legionella hackeliae in complex with acetyl-CoA

PDB DOI: https://doi.org/10.2210/pdb6WQB/pdb

Classification: TRANSFERASE
Organism(s): Legionella hackeliae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-04-28 Released: 2021-11-10
Deposition Author(s): Stogios, P.J., Skarina, T., Wawrzak, Z., Sandoval, J., Di Leo, R., Savchenko, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.214 (Depositor), 0.214 (DCC)
R-Value Work:
0.184 (Depositor), 0.185 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of VipF from Legionella hackeliae in complex with acetyl-CoA

Stogios, P.J.

To be published.

Macromolecule Content

Total Structure Weight: 35.27 kDa
Atom Count: 2,734
Modeled Residue Count: 290
Deposited Residue Count: 293
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-terminal acetyltransferase, GNAT family	A	293	Legionella hackeliae	Mutation(s): 0 Gene Names: vipF, LHA_0223
UniProt
Find proteins for A0A0A8UKD4 (Legionella hackeliae) Explore A0A0A8UKD4 Go to UniProtKB: A0A0A8UKD4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0A8UKD4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO (Subject of Investigation/LOI) Query on ACO 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]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.214 (Depositor), 0.214 (DCC)
R-Value Work: 0.184 (Depositor), 0.185 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.586	α = 90
b = 36.427	β = 90
c = 59.343	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-11-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-11-10
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

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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.