[English] 日本語
Yorodumi
- PDB-4fgz: Crystal Structure of Phosphoethanolamine Methyltransferase from P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fgz
TitleCrystal Structure of Phosphoethanolamine Methyltransferase from Plasmodium falciparum in Complex with Amodiaquine
ComponentsPhosphoethanolamine N-methyltransferase
KeywordsTRANSFERASE / SAM-dependent methyltransferase / SAM binding / methylation
Function / homology
Function and homology information


phosphomethylethanolamine N-methyltransferase activity / phosphoethanolamine N-methyltransferase activity / phosphoethanolamine N-methyltransferase / phosphatidylcholine biosynthetic process / methylation / Golgi membrane / Golgi apparatus
Similarity search - Function
Methyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CQA / PHOSPHATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Phosphoethanolamine N-methyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.994 Å
AuthorsLee, S.G. / Alpert, T.D. / Jez, J.M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: Crystal structure of phosphoethanolamine methyltransferase from Plasmodium falciparum in complex with amodiaquine.
Authors: Lee, S.G. / Alpert, T.D. / Jez, J.M.
History
DepositionJun 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoethanolamine N-methyltransferase
B: Phosphoethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,55010
Polymers62,1682
Non-polymers2,3828
Water3,441191
1
A: Phosphoethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2755
Polymers31,0841
Non-polymers1,1914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2755
Polymers31,0841
Non-polymers1,1914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.051, 60.639, 68.151
Angle α, β, γ (deg.)90.000, 90.008, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-421-

HOH

21A-440-

HOH

31B-426-

HOH

41B-458-

HOH

-
Components

#1: Protein Phosphoethanolamine N-methyltransferase /


Mass: 31084.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PMT / Production host: Escherichia coli (E. coli)
References: UniProt: Q6T755, phosphoethanolamine N-methyltransferase
#2: Chemical
ChemComp-CQA / 4-[(7-CHLOROQUINOLIN-4-YL)AMINO]-2-[(DIETHYLAMINO)METHYL]PHENOL / AMODIAQUINE / FLAVOQUINE / Amodiaquine


Mass: 355.861 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H22ClN3O / Comment: medication*YM
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG8000, 0.1 M sodium cacodylate, pH 6.5, 0.2 M sodium acetate, 5 mM beta-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2011
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→34.1 Å / Num. obs: 34098 / % possible obs: 92.4 % / Redundancy: 3.6 % / Rsym value: 0.067 / Net I/σ(I): 19.7
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.99-2.022.9211890.358165.8
2.02-2.063.12.213610.334172.3
2.06-2.13.32.913270.3174.2
2.1-2.143.33.313970.256176.6
2.14-2.193.43.615310.246182.8
2.19-2.243.43.916020.223187.7
2.24-2.33.54.517180.213192.7
2.3-2.363.65.218010.19198.2
2.36-2.433.76.118430.184199.5
2.43-2.513.87.118150.167199.7
2.51-2.63.8818170.148199.6
2.6-2.73.810.418490.118199.7
2.7-2.823.81218320.109199.8
2.82-2.973.814.818610.089199.7
2.97-3.163.819.618370.072199.9
3.16-3.43.824.418640.0631100
3.4-3.753.830.318440.0571100
3.75-4.293.734.118610.0561100
4.29-5.43.736.318690.0431100
5.4-34.13.737.419210.038199.3

-
Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.994→34.075 Å / SU ML: 0.26 / σ(F): 1.35 / σ(I): 2 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1709 5.01 %RANDOM
Rwork0.1807 ---
obs0.1831 34098 92.3 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.221 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.5081 Å20 Å2-0.3351 Å2
2--24.1021 Å20 Å2
3----14.5941 Å2
Refinement stepCycle: LAST / Resolution: 1.994→34.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4248 0 162 191 4601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074516
X-RAY DIFFRACTIONf_angle_d1.0076085
X-RAY DIFFRACTIONf_dihedral_angle_d20.3631733
X-RAY DIFFRACTIONf_chiral_restr0.07629
X-RAY DIFFRACTIONf_plane_restr0.004759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.994-2.05260.28141160.251954X-RAY DIFFRACTION68
2.0526-2.11880.29691170.23112147X-RAY DIFFRACTION74
2.1188-2.19450.2671340.20072328X-RAY DIFFRACTION80
2.1945-2.28240.24361480.19972572X-RAY DIFFRACTION89
2.2824-2.38620.21921580.19882838X-RAY DIFFRACTION98
2.3862-2.5120.26681470.19192899X-RAY DIFFRACTION99
2.512-2.66930.23631460.19722910X-RAY DIFFRACTION100
2.6693-2.87530.24811350.18182941X-RAY DIFFRACTION100
2.8753-3.16450.25281630.18182905X-RAY DIFFRACTION100
3.1645-3.6220.21211440.17792932X-RAY DIFFRACTION100
3.622-4.56160.22921450.15982971X-RAY DIFFRACTION100
4.5616-34.08050.18451560.17082992X-RAY DIFFRACTION99
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)
13.2655-0.0761-0.19741.3531-0.23783.3996-0.0460.5268-0.0045-0.1638-0.03490.09080.2304-0.51120.02640.2586-0.03870.03490.3155-0.01580.209721.494226.963419.9751
23.03470.06420.21561.354-0.15083.1732-0.0639-0.48410.01560.15460.0060.0764-0.2533-0.48820.01410.23440.036-0.04110.3034-0.01970.19254.432653.818214.0185
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

+
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