3FWZ | pdb_00003fwz

Crystal structure of TrkA-N domain of inner membrane protein ybaL from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb3FWZ/pdb

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


• Deposited: 2009-01-19 Released: 2009-02-10 
• Deposition Author(s): Chang, C., Bigelow, L., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.202 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Crystal structure of TrkA-N domain of inner membrane protein ybaL from Escherichia coli

Chang, C., Bigelow, L., Buck, K., Joachimiak, A.

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: 31.73 kDa 
• Atom Count: 2,418 
• Modeled Residue Count: 275 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inner membrane protein ybaL	A, B	140	Escherichia coli K-12	Mutation(s): 0  Gene Names: b0478, Escherichia coli CFT073, JW0467, ybaL, ylaA
UniProt
Find proteins for P39830 (Escherichia coli (strain K12)) Explore P39830  Go to UniProtKB:  P39830

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth A], D [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
MG	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 1.79 Å
• R-Value Free:  0.202 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.801	α = 90
b = 53.071	β = 97.82
c = 72.537	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
Coot	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-10 
Deposition Author(s): Chang, C., Bigelow, L., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-02-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary