4KBX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.599 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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

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

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein YhfX
A
388Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: yhfX
Find proteins for P45550 (Escherichia coli (strain K12))
Go to UniProtKB:  P45550
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
LLP
Query on LLP
A
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.599 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 66.920α = 90.00
b = 82.651β = 90.00
c = 149.460γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
PHENIXrefinement
HKL-2000data reduction
PHENIXphasing
HKL-2000data scaling
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-21
    Type: Initial release