[English] 日本語
Yorodumi
- PDB-9fqn: Crystal structure of phosphoserine phosphatase (SerB) from Brucel... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fqn
TitleCrystal structure of phosphoserine phosphatase (SerB) from Brucella melitensis in complex with L-Ser and Magnesium
ComponentsPhosphoserine phosphatase
KeywordsHYDROLASE / Complex / Serine biosynthesis / Magnesium cofactor / L-Serine / Product
Function / homology
Function and homology information


phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine biosynthetic process / magnesium ion binding / cytoplasm
Similarity search - Function
haloacid dehalogenase-like hydrolase / Phosphoserine phosphatase / : / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / SERINE / Phosphoserine phosphatase
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsScaillet, T. / Wouters, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proteins / Year: 2025
Title: Structural and Enzymological Characterization of Phosphoserine Phosphatase From Brucella melitensis.
Authors: Scaillet, T. / Pierson, E. / Fillet, M. / Wouters, J.
History
DepositionJun 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0548
Polymers32,5491
Non-polymers5057
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-26 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.830, 142.830, 142.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Space group name HallI2b2c3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z+1/2,x
#5: z,-x,-y+1/2
#6: -y+1/2,z,-x
#7: -z,-x+1/2,y
#8: -z+1/2,x,-y
#9: y,-z,-x+1/2
#10: x,-y,-z+1/2
#11: -x+1/2,y,-z
#12: -x,-y+1/2,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1,x+1/2
#17: z+1/2,-x+1/2,-y+1
#18: -y+1,z+1/2,-x+1/2
#19: -z+1/2,-x+1,y+1/2
#20: -z+1,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1
#22: x+1/2,-y+1/2,-z+1
#23: -x+1,y+1/2,-z+1/2
#24: -x+1/2,-y+1,z+1/2
Components on special symmetry positions
IDModelComponents
11A-573-

HOH

21A-575-

HOH

31A-600-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Phosphoserine phosphatase / O-phosphoserine phosphohydrolase


Mass: 32549.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Gene: BMEI0615 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YI30, phosphoserine phosphatase

-
Non-polymers , 6 types, 209 molecules

#2: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 0.2M sodium malonate, 0.1M Bis-tris propane, PEG3350
PH range: 6.5 - 8.0 / Temp details: Room temperature

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.0439 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0439 Å / Relative weight: 1
ReflectionResolution: 2.11→45.17 Å / Num. obs: 27894 / % possible obs: 99.84 % / Redundancy: 40.1 % / Biso Wilson estimate: 48.65 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.08128 / Rpim(I) all: 0.01306 / Rrim(I) all: 0.08233 / Net I/σ(I): 35.36
Reflection shellResolution: 2.11→2.19 Å / Redundancy: 38.3 % / Rmerge(I) obs: 1.374 / Mean I/σ(I) obs: 2.78 / Num. unique obs: 2749 / CC1/2: 0.856 / CC star: 0.96 / Rpim(I) all: 0.2232 / Rrim(I) all: 1.393 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→45.17 Å / SU ML: 0.3229 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.8999
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2477 1394 5 %
Rwork0.1961 26495 -
obs0.1987 27889 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.17 Å2
Refinement stepCycle: LAST / Resolution: 2.11→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 30 202 2425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752281
X-RAY DIFFRACTIONf_angle_d0.85353089
X-RAY DIFFRACTIONf_chiral_restr0.0518370
X-RAY DIFFRACTIONf_plane_restr0.0072404
X-RAY DIFFRACTIONf_dihedral_angle_d6.8219338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.190.40441370.35782611X-RAY DIFFRACTION98.6
2.19-2.270.28431390.28662632X-RAY DIFFRACTION99.96
2.28-2.380.29031380.24612614X-RAY DIFFRACTION99.96
2.38-2.50.29941390.24562645X-RAY DIFFRACTION100
2.5-2.660.34991390.26882645X-RAY DIFFRACTION100
2.66-2.870.27761380.25982618X-RAY DIFFRACTION100
2.87-3.150.27231390.22382648X-RAY DIFFRACTION100
3.15-3.610.26691400.20452660X-RAY DIFFRACTION100
3.61-4.540.19571400.15272655X-RAY DIFFRACTION100
4.55-45.170.2131450.15232767X-RAY DIFFRACTION99.93

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more