5I0C | pdb_00005i0c

Crystal structure of predicted acyltransferase YjdJ with acyl-CoA N-acyltransferase domain from Escherichia coli str. K-12

• PDB DOI: https://doi.org/10.2210/pdb5I0C/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-03 Released: 2016-02-24 
• Deposition Author(s): Filippova, E.V., Minasov, G., Wawrzak, Z., Shuvalova, L., Dubrovska, I., Winsor, J., Grimshaw, S., Wolfe, A.J., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.266 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Literature

Crystal structure of predicted acyltransferase YjdJ with acyl-CoA N-acyltransferase domain from Escherichia coli str. K-12

Filippova, E.V., Minasov, G., Wawrzak, Z., Shuvalova, L., Dubrovska, I., Winsor, J., Grimshaw, S., Wolfe, A.J., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.24 kDa 
• Atom Count: 794 
• Modeled Residue Count: 89 
• Deposited Residue Count: 93 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein YjdJ	A	93	Escherichia coli K-12	Mutation(s): 0  Gene Names: yjdJ, b4127, JW4088
UniProt
Find proteins for P39274 (Escherichia coli (strain K12)) Explore P39274  Go to UniProtKB:  P39274

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	E [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
PO4	F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NI	B [auth A], C [auth A], D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.266 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35i0c

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.69	α = 90
b = 87.84	β = 90
c = 41.58	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
PHENIX	phasing
PHENIX	model building
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-24 
Deposition Author(s): Filippova, E.V., Minasov, G., Wawrzak, Z., Shuvalova, L., Dubrovska, I., Winsor, J., Grimshaw, S., Wolfe, A.J., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-02-24
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary