[English] 日本語
Yorodumi
- PDB-8a21: Crystal structure of Phosphoserine phosphatase SerB from Mycobact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a21
TitleCrystal structure of Phosphoserine phosphatase SerB from Mycobacterium avium in complex with phenylimidazole
ComponentsPhosphoserine phosphatase
KeywordsHYDROLASE / phosphoserine phosphatase / avium / PIM / phenylimidazole
Function / homology
Function and homology information


phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine biosynthetic process / metal ion binding
Similarity search - Function
Phosphoserine phosphatase / ACT domain profile. / ACT domain / ACT-like domain / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
4-PHENYL-1H-IMIDAZOLE / Phosphoserine phosphatase
Similarity search - Component
Biological speciesMycobacterium avium 104 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.18 Å
AuthorsHaufroid, M. / Wouters, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Targeting the phosphoserine phosphatase MtSerB2 for tuberculosis drug discovery, an hybrid knowledge based /fragment based approach.
Authors: Haufroid, M. / Volkov, A.N. / Wouters, J.
History
DepositionJun 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2926
Polymers43,8521
Non-polymers4405
Water3,801211
1
A: Phosphoserine phosphatase
hetero molecules

A: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,58512
Polymers87,7042
Non-polymers88010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area8570 Å2
ΔGint-55 kcal/mol
Surface area29410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.570, 109.740, 133.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Phosphoserine phosphatase / O-phosphoserine phosphohydrolase


Mass: 43852.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium 104 (bacteria) / Gene: O972_03940 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V7LE91, phosphoserine phosphatase

-
Non-polymers , 5 types, 216 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PIM / 4-PHENYL-1H-IMIDAZOLE


Mass: 144.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8N2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.1 / Details: MgCl2 0,5M; 20%PEG6000 MES 0.1M pH6.1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.18→43.09 Å / Num. obs: 25224 / % possible obs: 98.76 % / Redundancy: 13.3 % / Biso Wilson estimate: 35.66 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1115 / Rpim(I) all: 0.0319 / Rrim(I) all: 0.1161 / Net I/σ(I): 16.22
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 11.6 % / Rmerge(I) obs: 1.531 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 2238 / CC1/2: 0.777 / CC star: 0.935 / Rpim(I) all: 0.4595 / % possible all: 87.94

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3p96

3p96


Resolution: 2.18→43.09 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2705 2000 7.93 %
Rwork0.2059 23222 -
obs0.211 25222 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.82 Å2 / Biso mean: 37.0195 Å2 / Biso min: 16.97 Å2
Refinement stepCycle: final / Resolution: 2.18→43.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2845 0 38 211 3094
Biso mean--44.69 41.22 -
Num. residues----396
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.18-2.240.39951180.37321363148183
2.24-2.30.35651420.312316601802100
2.3-2.370.31661440.284716591803100
2.37-2.440.3381430.263716661809100
2.44-2.530.35611410.251416421783100
2.53-2.630.32461440.241216711815100
2.63-2.750.29061420.244916471789100
2.75-2.890.34541450.242216861831100
2.9-3.080.31311420.224516531795100
3.08-3.310.30661450.197216881833100
3.31-3.650.22671460.187516851831100
3.65-4.180.23781450.159316871832100
4.18-5.260.19791480.145617151863100
5.26-43.090.2381550.198718001955100

+
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