7QPL | pdb_00007qpl

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

PDB DOI: https://doi.org/10.2210/pdb7QPL/pdb

Classification: HYDROLASE
Organism(s): Brucella melitensis bv. 1 str. 16M
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2022-01-05 Released: 2023-01-18
Deposition Author(s): Pierson, E., Wouters, J.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.183 (Depositor), 0.186 (DCC)
R-Value Work:
0.158 (Depositor), 0.165 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 7QPL

This is version 1.2 of the entry. See complete history.

Literature

Structural and Enzymological Characterization of Phosphoserine Phosphatase From Brucella melitensis

Pierson, E., Wouters, J.

(2025) Proteins

DOI: https://doi.org/10.1002/prot.70027

Macromolecule Content

Total Structure Weight: 33.68 kDa
Atom Count: 2,573
Modeled Residue Count: 295
Deposited Residue Count: 307
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-phosphoserine phosphohydrolase	A	307	Brucella melitensis bv. 1 str. 16M	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8YI30
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth A]	C [auth A] E [auth A] I [auth A] J [auth A] K [auth A] C [auth A], E [auth A], I [auth A], J [auth A], K [auth A], N [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth A] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	L [auth A], M [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain O [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth A]	D [auth A], F [auth A], G [auth A], H [auth A], O [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth A] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.183 (Depositor), 0.186 (DCC)
R-Value Work: 0.158 (Depositor), 0.165 (DCC)

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.21	α = 90
b = 143.21	β = 90
c = 143.21	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Belgium	--

Revision History (Full details and data files)

Version 1.0: 2023-01-18
Type: Initial release
Version 1.1: 2024-05-01
Changes: Data collection, Refinement description
Version 1.2: 2025-08-06
Changes: Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.