1S7D | pdb_00001s7d

Crystal structure of refined tetragonal crystal of YodA from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb1S7D/pdb

• Classification: STRUCTURAL GENOMICS
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-01-29 Released: 2004-08-10 
• Deposition Author(s): Shin, D.H., Yokota, H., Kim, R., Kim, S.H., Berkeley Structural Genomics Center (BSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.255 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Crystal structure of refined tetragonal crystal of YodA from Escherichia coli

Shin, D.H., Yokota, H., Kim, R., Kim, S.H.

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)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.06 kDa 
• Atom Count: 1,614 
• Modeled Residue Count: 187 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal-binding Protein yodA	A	216	Escherichia coli	Mutation(s): 0  Gene Names: yodA
UniProt
Find proteins for P76344 (Escherichia coli (strain K12)) Explore P76344  Go to UniProtKB:  P76344

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.255 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.009	α = 90
b = 55.009	β = 90
c = 153.785	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-10 
Deposition Author(s): Shin, D.H., Yokota, H., Kim, R., Kim, S.H., Berkeley Structural Genomics Center (BSGC)

Revision History  

• Version 1.0: 2004-08-10
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary