3M1Y | pdb_00003m1y

Crystal Structure of a Phosphoserine phosphatase (SerB) from Helicobacter pylori

• PDB DOI: https://doi.org/10.2210/pdb3M1Y/pdb

• Classification: HYDROLASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-03-05 Released: 2010-03-23 
• Deposition Author(s): Syed Ibrahim, B., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.271 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Literature

Crystal Structure of a Phosphoserine phosphatase (SerB) from Helicobacter pylori

Syed Ibrahim, B., Burley, S.K., Swaminathan, S.

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: 98.56 kDa 
• Atom Count: 6,500 
• Modelled Residue Count: 823 
• Deposited Residue Count: 868 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoserine phosphatase (SerB)	A, B, C, D	217	Helicobacter pylori	Mutation(s): 0  Gene Names: HP_0652 EC: 3.1.3.3
UniProt
Find proteins for O25367 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25367  Go to UniProtKB:  O25367

Small Molecules

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.271 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.607	α = 90
b = 84.719	β = 90
c = 204.826	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELX	model building
SHARP	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-23 
Deposition Author(s): Syed Ibrahim, B., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Structure summary