1YIX | pdb_00001yix

Crystal structure of YCFH, TATD homolog from Escherichia coli K12, at 1.9 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1YIX/pdb

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


• Deposited: 2005-01-13 Released: 2005-01-25 
• Deposition Author(s): Malashkevich, V.N., Xiang, D.F., Raushel, F.M., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.252 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of ycfH, tatD homolog from Escherichia coli

Malashkevich, V.N., Xiang, D.F., Raushel, F.M., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 60.02 kDa 
• Atom Count: 4,766 
• Modeled Residue Count: 530 
• Deposited Residue Count: 530 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
deoxyribonuclease ycfH	A, B	265	Escherichia coli K-12	Mutation(s): 0  Gene Names: ycfH EC: 3.1.21 (PDB Primary Data), 3.1 (UniProt)
UniProt
Find proteins for P0AFQ7 (Escherichia coli (strain K12)) Explore P0AFQ7  Go to UniProtKB:  P0AFQ7

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.252 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.387	α = 90
b = 76.322	β = 92.3
c = 80.738	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-25 
Deposition Author(s): Malashkevich, V.N., Xiang, D.F., Raushel, F.M., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-01-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2023-08-23
  Changes: Data collection, Database references, Refinement description