[English] 日本語
Yorodumi
- PDB-9hsx: Crystal structure of C-terminal catalytic domain of Plasmodium fa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hsx
TitleCrystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 2-aminopyridine
Componentscholine-phosphate cytidylyltransferase
KeywordsTRANSFERASE / CCT
Function / homology
Function and homology information


Synthesis of PC / choline-phosphate cytidylyltransferase / choline-phosphate cytidylyltransferase activity / phosphatidylcholine binding / identical protein binding
Similarity search - Function
Choline-phosphate cytidylyltransferase Pcy1-like / CTP:phosphocholine cytidylyltransferase domain / Cytidylyltransferase-like / Cytidyltransferase-like domain / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
pyridin-2-amine / choline-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsAudebert, S. / Gelin, M. / Guichou, J.-F.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE44-0012 France
CitationJournal: To Be Published
Title: Crystal structure of C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 2-aminopyridine
Authors: Audebert, S. / Gelin, M. / Guichou, J.-F.
History
DepositionDec 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8353
Polymers20,6471
Non-polymers1882
Water57632
1
A: choline-phosphate cytidylyltransferase
hetero molecules

A: choline-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6706
Polymers41,2942
Non-polymers3764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area2030 Å2
ΔGint-7 kcal/mol
Surface area13970 Å2
Unit cell
Length a, b, c (Å)50.354, 70.945, 119.638
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein choline-phosphate cytidylyltransferase


Mass: 20646.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Deletion of a lysine rich loop (720 - 737)
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF3D7_1316600 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8IEE9, choline-phosphate cytidylyltransferase
#2: Chemical ChemComp-HVK / pyridin-2-amine


Mass: 94.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350 11.5%, NaF 210 mM, Glycerol 5.8%, MnCl2 15mM, 1,3 propandiol 3%

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 2.23→46.41 Å / Num. obs: 17730 / % possible obs: 95.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 48.54 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.047 / Rrim(I) all: 0.098 / Χ2: 1.12 / Net I/σ(I): 9
Reflection shellResolution: 2.23→2.3 Å / % possible obs: 86.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 1.006 / Num. measured all: 2767 / Num. unique obs: 824 / CC1/2: 0.529 / Rpim(I) all: 0.62 / Rrim(I) all: 1.19 / Χ2: 1.25 / Net I/σ(I) obs: 1.5

-
Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→46.41 Å / SU ML: 0.367 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.3248
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2735 901 5.08 %
Rwork0.2112 16829 -
obs0.2141 17730 87.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.39 Å2
Refinement stepCycle: LAST / Resolution: 2.23→46.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 0 14 32 1094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711090
X-RAY DIFFRACTIONf_angle_d0.81411478
X-RAY DIFFRACTIONf_chiral_restr0.0494170
X-RAY DIFFRACTIONf_plane_restr0.0063184
X-RAY DIFFRACTIONf_dihedral_angle_d15.0519390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.370.35371310.37622394X-RAY DIFFRACTION75.46
2.37-2.550.31991530.29842905X-RAY DIFFRACTION90.69
2.55-2.810.29981320.26942896X-RAY DIFFRACTION90.33
2.81-3.220.29721640.25942930X-RAY DIFFRACTION91.38
3.22-4.050.25571710.19712837X-RAY DIFFRACTION90.28
4.05-46.410.25531500.16392867X-RAY DIFFRACTION88.94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.43225871208-0.4383950298890.896781616374.64897905971-1.237670318333.58828642245-0.0322489447315-0.3194215234480.3802038741520.275733320348-0.04373547585-0.00839993152168-0.161190325478-0.1485868824560.06943287930240.3016909994480.004024376490780.02867492125120.331219176707-0.03023995219180.342378682945-2.61504345775-22.2432491154-24.1571779773
25.54084169538-4.77315430191-3.270162637514.782832530864.734673605787.40984046387-1.08227036304-0.9627559370420.02814849247032.18600271317-0.08989098267810.8114679509211.18068196079-1.248379754430.6296102798480.9150208629970.03664082674990.03184463600140.990671256370.03844328362560.628202262105-14.0330581408-18.2095686915-21.4396194121
32.414897387643.395869621630.6813825689578.246648471712.090288880038.910214859630.22175118257-2.149701079041.317625255861.58444460314-0.0327198636717-1.48659796536-0.2724003431630.461019952803-0.1728545718090.6308839339970.0706436087833-0.2022502543650.909134675685-0.2097926845230.769117999982-15.811339382-10.5670185582-25.5564357966
43.54934948963-4.844568905645.761801409867.18147443515-8.234239629979.5596064353-0.868123083559-0.9235562708950.4354832812420.7401147096240.771799765855-0.75069071-0.424591891181-1.46406717897-0.2802845411940.6788285423310.03435906530290.01911362272660.980726526629-0.2373187590430.567231833736-9.95159310634-32.703592042-12.0181390995
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 616 through 706 )616 - 7061 - 91
22chain 'A' and (resid 707 through 739 )707 - 73992 - 97
33chain 'A' and (resid 740 through 747 )740 - 74798 - 105
44chain 'A' and (resid 748 through 774 )748 - 772106 - 130

+
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