1J2R | pdb_00001j2r

Crystal structure of Escherichia coli gene product Yecd at 1.3 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1J2R/pdb

• Classification: Structural genomics, unknown function
• Organism(s): Escherichia coli
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2003-01-09 Released: 2004-01-27 
• Deposition Author(s): Suhre, K., Claverie, J.-M., Abergel, C., Bacterial targets at IGS-CNRS, France (BIGS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of escherichia coli gene product Yecd at 1.3 A resolution

Suhre, K., Claverie, J.-M., Abergel, C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 88.6 kDa 
• Atom Count: 6,771 
• Modeled Residue Count: 748 
• Deposited Residue Count: 796 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical isochorismatase family protein yecD	A, B, C, D	199	Escherichia coli	Mutation(s): 1  Gene Names: yecD EC: 3
UniProt
Find proteins for P0ADI7 (Escherichia coli (strain K12)) Explore P0ADI7  Go to UniProtKB:  P0ADI7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B], K [auth C], L [auth C], M [auth C], N [auth D], O [auth D], P [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.502	α = 90
b = 108.886	β = 90
c = 50.419	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
TRUNCATE	data scaling
T-COFFEE	phasing
MODELLER	phasing
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-01-27 
Deposition Author(s): Suhre, K., Claverie, J.-M., Abergel, C., Bacterial targets at IGS-CNRS, France (BIGS)

Revision History  

• Version 1.0: 2004-01-27
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.5: 2023-10-25
  Changes: Data collection, Refinement description