1W8G | pdb_00001w8g

CRYSTAL STRUCTURE OF E. COLI K-12 YGGS

• PDB DOI: https://doi.org/10.2210/pdb1W8G/pdb

• Classification: PLP-BINDING PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-09-21 Released: 2006-07-05 
• Deposition Author(s): Sulzenbacher, G., Gruez, A., Spinelli, S., Roig-Zamboni, V., Pagot, F., Bignon, C., Vincentelli, R., Cambillau, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.195 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of E. Coli K-12 Yggs

Sulzenbacher, G., Gruez, A., Spinelli, S., Roig-Zamboni, V., Pagot, F., Bignon, C., Vincentelli, R., Cambillau, C.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 26.26 kDa 
• Atom Count: 2,102 
• Modeled Residue Count: 226 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOTHETICAL UPF0001 PROTEIN YGGS	A	234	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P67080 (Escherichia coli (strain K12)) Explore P67080  Go to UniProtKB:  P67080

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
ICT	C [auth A]	ISOCITRIC ACID C6 H8 O7 ODBLHEXUDAPZAU-ZAFYKAAXSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.195 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.017	α = 90
b = 124.017	β = 90
c = 83.729	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-05 
Deposition Author(s): Sulzenbacher, G., Gruez, A., Spinelli, S., Roig-Zamboni, V., Pagot, F., Bignon, C., Vincentelli, R., Cambillau, C.

Revision History  

• Version 1.0: 2006-07-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description