3EXM | pdb_00003exm

Crystal structure of the phosphatase SC4828 with the non-hydrolyzable nucleotide GPCP

• PDB DOI: https://doi.org/10.2210/pdb3EXM/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces coelicolor A3(2)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-16 Released: 2008-12-09 
• Deposition Author(s): Singer, A.U., Xu, X., Zheng, H., Joachimiak, A., Edwards, A.M., Savchenko, A., Yakunin, A.F., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.199 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Structure and mechanism of a new family of prokaryotic nucleoside diphosphatases.

Proudfoot, M., Brown, M., Singer, A.U., Jobin, M.-C., Xu, X., Zheng, H., Chang, C., Edwards, A.M., Joachimiak, A., Savchenko, A., Yakunin, A.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.21 kDa 
• Atom Count: 2,145 
• Modeled Residue Count: 210 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatase SC4828	A	237	Streptomyces coelicolor A3(2)	Mutation(s): 0  Gene Names: SCO5041, SCK7.14, SCK7.14c EC: 3.6.1.6
UniProt
Find proteins for Q9FBN7 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9FBN7  Go to UniProtKB:  Q9FBN7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GP2	G [auth A]	PHOSPHOMETHYLPHOSPHONIC ACID GUANOSYL ESTER C11 H17 N5 O10 P2 OCJWYBKRHNXUME-KQYNXXCUSA-N
GOL	H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.199 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.941	α = 90
b = 79.706	β = 90
c = 82.507	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-09 
Deposition Author(s): Singer, A.U., Xu, X., Zheng, H., Joachimiak, A., Edwards, A.M., Savchenko, A., Yakunin, A.F., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-12-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description