4J8L | pdb_00004j8l

CRYSTAL STRUCTURE OF THE PYRIDOXAL-5'-PHOSPHATE DEPENDENT protein YhfS from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb4J8L/pdb

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


• Deposited: 2013-02-14 Released: 2014-03-05 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Xiang, D.F., Raushel, F.M., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.195 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Crystal structure of the pyridoxal-5'-phosphate dependent protein yhfs from escherichia coli

Fedorov, A.A., Fedorov, E.V., Xiang, D.F., Raushel, F.M., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.4 kDa 
• Atom Count: 3,051 
• Modeled Residue Count: 361 
• Deposited Residue Count: 361 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein YhfS	A	361	Escherichia coli K-12	Mutation(s): 0  Gene Names: yhfS, b3376, JW3339
UniProt
Find proteins for P45545 (Escherichia coli (strain K12)) Explore P45545  Go to UniProtKB:  P45545

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACY	C [auth A], D [auth A], E [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.195 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.915	α = 90
b = 134.915	β = 90
c = 75.142	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-05 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Xiang, D.F., Raushel, F.M., Almo, S.C.

Revision History  

• Version 1.0: 2014-03-05
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary