8VR6 | pdb_00008vr6

crystal structure of the Pcryo_0619 N-acetryltransferase from Psychrobacter cryohalolentis K5 in the presence of CoA-disulfide

PDB DOI: https://doi.org/10.2210/pdb8VR6/pdb

Classification: TRANSFERASE
Organism(s): Psychrobacter cryohalolentis K5
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-01-20 Released: 2024-01-31
Deposition Author(s): Dunsirn, M.M., Bockhaus, N.J., Thoden, J.B., Holden, H.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.242 (Depositor), 0.256 (DCC)
R-Value Work:
0.202 (Depositor)
R-Value Observed:
0.205 (Depositor)

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Ligand Structure Quality Assessment

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Literature

Biochemical Investigation of the Enzymes Required for the Production of 2,3,4-triacetoamido-2,3,4-trideoxy-l-arabinose in Psychrobacter cryohalolentis K5

Bockhaus, N.J., Dunsirn, M.M., Thoden, J.B., Holden, H.M.

To be published.

Macromolecule Content

Total Structure Weight: 21.13 kDa
Atom Count: 1,497
Modeled Residue Count: 177
Deposited Residue Count: 182
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyltransferase, putative	A	182	Psychrobacter cryohalolentis K5	Mutation(s): 0 Gene Names: Pcryo_0619
UniProt
Find proteins for Q1QD51 (Psychrobacter cryohalolentis (strain ATCC BAA-1226 / DSM 17306 / VKM B-2378 / K5)) Explore Q1QD51 Go to UniProtKB: Q1QD51
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q1QD51
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5NG (Subject of Investigation/LOI) Query on 5NG 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]	[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyldisulfanyl]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate C₄₂ H₇₀ N₁₄ O₃₂ P₆ S₂ YAISMNQCMHVVLO-BJLFRJKCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.242 (Depositor), 0.256 (DCC)
R-Value Work: 0.202 (Depositor)
R-Value Observed: 0.205 (Depositor)

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.903	α = 90
b = 114.903	β = 90
c = 114.903	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELXDE	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-01-31

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM134643

Revision History (Full details and data files)

Version 1.0: 2024-01-31
Type: Initial release

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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.