4RS2 | pdb_00004rs2

1.55 Angstrom Crystal Structure of GNAT Family N-acetyltransferase (YhbS) from Escherichia coli in Complex with CoA

PDB DOI: https://doi.org/10.2210/pdb4RS2/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli str. K-12 substr. MG1655
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2014-11-06 Released: 2014-11-19
Deposition Author(s): Minasov, G., Wawrzak, Z., Kuhn, M., Shuvalova, L., Dubrovska, I., Flores, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.203 (Depositor), 0.212 (DCC)
R-Value Work:
0.164 (Depositor), 0.174 (DCC)
R-Value Observed:
0.166 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

1.55 Angstrom Crystal Structure of GNAT Family N-acetyltransferase (YhbS) from Escherichia coli in Complex with CoA.

Minasov, G., Wawrzak, Z., Kuhn, M., Shuvalova, L., Dubrovska, I., Flores, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 43.33 kDa
Atom Count: 3,717
Modeled Residue Count: 363
Deposited Residue Count: 376
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted acyltransferase with acyl-CoA N-acyltransferase domain	A, B	188	Escherichia coli str. K-12 substr. MG1655	Mutation(s): 0 Gene Names: ECMDS42_2623, yhbS

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.203 (Depositor), 0.212 (DCC)
R-Value Work: 0.164 (Depositor), 0.174 (DCC)
R-Value Observed: 0.166 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.863	α = 80.4
b = 44.658	β = 80.25
c = 57.023	γ = 90.17

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-11-19

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2014-11-19
Type: Initial release
Version 1.1: 2015-01-21
Changes: Data collection
Version 1.2: 2017-11-22
Changes: Refinement description
Version 1.3: 2024-11-06
Changes: 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.