3CBT | pdb_00003cbt

Crystal structure of SC4828, a unique phosphatase from Streptomyces coelicolor

• PDB DOI: https://doi.org/10.2210/pdb3CBT/pdb
• Entry: 3CBT supersedes: 3BXT

• Classification: HYDROLASE
• Organism(s): Streptomyces coelicolor A3(2)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-02-22 Released: 2008-03-25 
• Deposition Author(s): Singer, A.U., Xu, X., Chang, C., Zheng, H., Edwards, A.M., Joachimiak, A., Yakunin, A.F., Savchenko, 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: 
  0.215 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Crystal structure of SC4828, a unique phosphatase from Streptomyces coelicolor.

Singer, A.U., Proudfoot, M., Brown, G., Xu, X., Chang, C., Zhang, H., 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 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.69 kDa 
• Atom Count: 2,059 
• 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, gi:21223414 EC: 3.1.3.5
UniProt
Find proteins for Q9FBN7 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9FBN7  Go to UniProtKB:  Q9FBN7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	C [auth A], D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.215 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.738	α = 90
b = 77.271	β = 90
c = 80.044	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Singer, A.U., Xu, X., Chang, C., Zheng, H., Edwards, A.M., Joachimiak, A., Yakunin, A.F., Savchenko, A., Midwest Center for Structural Genomics (MCSG)
• This entry supersedes: 3BXT

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary