8Q4S | pdb_00008q4s

Crystal structure of phosphoserine phosphatase (SerB) from Brucella melitensis in complex with AP4 and magnesium.

• PDB DOI: https://doi.org/10.2210/pdb8Q4S/pdb

• Classification: HYDROLASE
• Organism(s): Brucella melitensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-08-07 Released: 2024-08-21 
• Deposition Author(s): Scaillet, T., Wouters, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.225 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of phosphoserine phosphatase (SerB) from Brucella melitensis in complex with AP4 and magnesium.

Scaillet, T., Wouters, J.

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)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 32.94 kDa 
• Atom Count: 2,437 
• Modeled Residue Count: 295 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoserine phosphatase	A	307	Brucella melitensis	Mutation(s): 0  Gene Names: BMEI0615 EC: 3.1.3.3
UniProt
Find proteins for Q8YI30 (Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)) Explore Q8YI30  Go to UniProtKB:  Q8YI30

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E7P (Subject of Investigation/LOI)	B [auth A]	(2S)-2-amino-4-phosphonobutanoic acid C4 H10 N O5 P DDOQBQRIEWHWBT-VKHMYHEASA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.225 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.08	α = 90
b = 144.08	β = 90
c = 144.08	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
XSCALE	data scaling
XDS	data reduction
Coot	model building
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-21 
Deposition Author(s): Scaillet, T., Wouters, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-08-21
  Type: Initial release