1YDF | pdb_00001ydf

Crystal structure of a HAD-like phosphatase from Streptococcus pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb1YDF/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-12-23 Released: 2005-01-18 
• Deposition Author(s): Seetharaman, J., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Crystal Structure of a Hypothetical protein, hydrolase haloacid dehalogenase-like family

Seetharaman, J., Swaminathan, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.21 kDa 
• Atom Count: 2,039 
• Modeled Residue Count: 255 
• Deposited Residue Count: 257 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hydrolase, haloacid dehalogenase-like family	A	257	Streptococcus pneumoniae TIGR4	Mutation(s): 0
UniProt
Find proteins for A0A0H2UQJ9 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UQJ9  Go to UniProtKB:  A0A0H2UQJ9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.43	α = 90
b = 99.929	β = 90
c = 39.841	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-18 
Deposition Author(s): Seetharaman, J., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-01-18
  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: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references