1RKQ | pdb_00001rkq

Crystal structure of HAD-like phosphatase yidA from E. coli

• PDB DOI: https://doi.org/10.2210/pdb1RKQ/pdb

• Classification: structural genomics, unknown function
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-11-23 Released: 2004-03-09 
• Deposition Author(s): Ramagopal, U.A., 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: 1.40 Å
• R-Value Free: 
  0.213 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.170 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of NYSGRC target T1436: A Hypothetical protein yidA.

Ramagopal, U.A., 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: 62.28 kDa 
• Atom Count: 4,830 
• Modeled Residue Count: 542 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein yidA	A, B	282	Escherichia coli	Mutation(s): 0  Gene Names: YIDA, B3697, C4619, SF3767, S4004 EC: 3.1.3.23
UniProt
Find proteins for P0A8Y5 (Escherichia coli (strain K12)) Explore P0A8Y5  Go to UniProtKB:  P0A8Y5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.213 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.170 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.12	α = 112.58
b = 54.871	β = 96.37
c = 67.725	γ = 106.79

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELXE	model building
RESOLVE	model building
ARP/wARP	model building
REFMAC	refinement
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-09 
Deposition Author(s): Ramagopal, U.A., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2004-03-09
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: 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: 2024-02-14
  Changes: Data collection, Database references
• Version 1.6: 2024-04-03
  Changes: Refinement description