1M68

YCDX PROTEIN, TRINUCLEAR ZINC SITE

• PDB DOI: https://doi.org/10.2210/pdb1M68/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-07-14 Released: 2003-04-22 
• Deposition Author(s): Teplyakov, A., Obmolova, G., Khil, P.P., Camerini-Otero, R.D., Gilliland, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.225 
• R-Value Work: 0.162 
• R-Value Observed: 0.165 

Starting Model: experimental

Literature

Crystal structure of the Escherichia coli YcdX protein reveals a trinuclear zinc active site

Teplyakov, A., Obmolova, G., Khil, P.P., Howard, A.J., Camerini-Otero, R.D., Gilliland, G.L.

(2003) Proteins 51: 315-318

• PubMed: 12661000 
• DOI: https://doi.org/10.1002/prot.10352
• Primary Citation of Related Structures:  
  1M65, 1M68

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Organizational Affiliation: 

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and the National Institute of Standards and Technology, Rockville, Maryland 20850, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 27.31 kDa 
• Atom Count: 2,009 
• Modelled Residue Count: 234 
• Deposited Residue Count: 245 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ycdX	A	245	Escherichia coli	Mutation(s): 0  EC: 3.1.3
UniProt
Find proteins for P75914 (Escherichia coli (strain K12)) Explore P75914  Go to UniProtKB:  P75914

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.225 
• R-Value Work: 0.162 
• R-Value Observed: 0.165 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.35	α = 90
b = 77.35	β = 90
c = 80.05	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-22 
Deposition Author(s): Teplyakov, A., Obmolova, G., Khil, P.P., Camerini-Otero, R.D., Gilliland, G.L.

Revision History  

• Version 1.0: 2003-04-22
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Refinement description