3RF6 | pdb_00003rf6

Crystal structure of glycerol-3 phosphate bound HAD-like phosphatase from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb3RF6/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-04-05 Released: 2011-06-01 
• Deposition Author(s): Nocek, B., Kuznetsova, K., Evdokimova, E., Savchenko, A., Iakunine, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Literature

Crystal structure of glycerol-3 phosphate bound HAD-like phosphatase from Saccharomyces cerevisiae

Nocek, B., Kuznetsova, K., Evdokimova, E., Savchenko, A., Iakunine, A., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 80.16 kDa 
• Atom Count: 6,017 
• Modeled Residue Count: 692 
• Deposited Residue Count: 710 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein YKR070W	A, B	355	Saccharomyces cerevisiae	Mutation(s): 1  Gene Names: YKR070W EC: 3
UniProt
Find proteins for P36151 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36151  Go to UniProtKB:  P36151

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	C [auth A], G [auth B]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
G3P	D [auth A], H [auth B]	SN-GLYCEROL-3-PHOSPHATE C3 H9 O6 P AWUCVROLDVIAJX-GSVOUGTGSA-N
MG	E [auth A], F [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.912	α = 90
b = 71.652	β = 90
c = 195.428	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-01 
Deposition Author(s): Nocek, B., Kuznetsova, K., Evdokimova, E., Savchenko, A., Iakunine, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2011-06-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2018-02-07
  Changes: Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references, Derived calculations