4JXR | pdb_00004jxr

Crystal structure of a GNAT superfamily phosphinothricin acetyltransferase (Pat) from Sinorhizobium meliloti in complex with AcCoA

• PDB DOI: https://doi.org/10.2210/pdb4JXR/pdb

• Classification: TRANSFERASE
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-03-28 Released: 2013-05-15 
• Deposition Author(s): Majorek, K.A., Cooper, D.R., Porebski, P.J., Konina, K., Ahmed, M., Stead, M., Hillerich, B., Seidel, R., Bonanno, J.B., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.137 (Depositor), 0.136 (DCC) 
• R-Value Work: 
  0.115 (Depositor), 0.114 (DCC) 
• R-Value Observed: 
  0.116 (Depositor) 

Literature

Crystal structure of a GNAT superfamily phosphinothricin acetyltransferase (Pat) from Sinorhizobium meliloti in complex with AcCoA

Majorek, K.A., Cooper, D.R., Porebski, P.J., Konina, K., Ahmed, M., Stead, M., Hillerich, B., Seidel, R., Bonanno, J.B., Almo, S.C., Minor, W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 42.47 kDa 
• Atom Count: 4,006 
• Modeled Residue Count: 370 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyltransferase	A, B	186	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: R03223, SMc03840 EC: 2.3.1
UniProt
Find proteins for Q92L60 (Rhizobium meliloti (strain 1021)) Explore Q92L60  Go to UniProtKB:  Q92L60

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACO	F [auth B]	ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N
2PE	D [auth A]	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N
FLC	C [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
PEG	E [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.137 (Depositor), 0.136 (DCC) 
• R-Value Work:  0.115 (Depositor), 0.114 (DCC) 
• R-Value Observed: 0.116 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M3W01C

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.256	α = 90
b = 80.978	β = 90
c = 83.87	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
ARP/wARP	model building
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-15 
Deposition Author(s): Majorek, K.A., Cooper, D.R., Porebski, P.J., Konina, K., Ahmed, M., Stead, M., Hillerich, B., Seidel, R., Bonanno, J.B., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-05-15
  Type: Initial release
  
• Version 1.1: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2024-11-20
  Changes: Data collection, Structure summary