[English] 日本語
Yorodumi
- PDB-5yg2: Plasmodium vivax SHMT bound with PLP-glycine and GS705 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yg2
TitlePlasmodium vivax SHMT bound with PLP-glycine and GS705
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE/INHIBITOR / alpha and beta protein / Transferase / methyltransferase activity / Inhibitor / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / methyltransferase activity / pyridoxal phosphate binding / methylation / mitochondrion
Similarity search - Function
: / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-N05 / Chem-PLG / glycine hydroxymethyltransferase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
Model detailsPlasmodium vivax SHMT bound with PLP-glycine and GS834
AuthorsChitnumsub, P. / Jaruwat, A. / Leartsakulpanich, U. / Schwertz, G. / Diederich, F.
CitationJournal: ChemMedChem / Year: 2018
Title: Potent Inhibitors of Plasmodial Serine Hydroxymethyltransferase (SHMT) Featuring a Spirocyclic Scaffold
Authors: Schwertz, G. / Witschel, M.C. / Rottmann, M. / Leartsakulpanich, U. / Chitnumsub, P. / Jaruwat, A. / Amornwatcharapong, W. / Ittarat, W. / Schafer, A. / Aponte, R.A. / Trapp, N. / Chaiyen, P. / Diederich, F.
History
DepositionSep 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
C: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,14011
Polymers147,7473
Non-polymers2,3928
Water4,414245
1
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0817
Polymers98,4982
Non-polymers1,5835
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint-52 kcal/mol
Surface area29780 Å2
MethodPISA
2
C: Serine hydroxymethyltransferase
hetero molecules

C: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1178
Polymers98,4982
Non-polymers1,6186
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area10110 Å2
ΔGint-81 kcal/mol
Surface area29610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.644, 58.682, 234.758
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Serine hydroxymethyltransferase


Mass: 49249.160 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVC01_140059500, PVP01_1453700, PVT01_140059000 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A1G4H5I1, glycine hydroxymethyltransferase
#2: Chemical ChemComp-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE


Mass: 306.209 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N2O7P
#3: Chemical ChemComp-N05 / 3-[1-[3-[(4~{S})-6-azanyl-5-cyano-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazol-4-yl]-5-fluoranyl-phenyl]piperidin-4-yl]propanoic acid


Mass: 467.536 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H30FN5O3
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.37 Å3/Da / Density % sol: 48.09 % / Mosaicity: 0.474 °
Crystal growTemperature: 298 K / Method: microbatch / pH: 8.5 / Details: PEG 4000, 0.06-0.12 M NaCl, 0.1 M Tris-HCl pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 70254 / % possible obs: 99.1 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.015 / Rrim(I) all: 0.034 / Χ2: 0.828 / Net I/σ(I): 20
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.284.30.33366610.9280.1730.3771.06894.5
2.28-2.375.50.25469740.970.1180.280.74699.9
2.37-2.485.50.18370620.9840.0850.2030.77399.9
2.48-2.615.50.12570100.990.0580.1380.78899.8
2.61-2.775.40.07970950.9940.0370.0880.79399.8
2.77-2.995.30.05170380.9950.0240.0570.76699.8
2.99-3.295.20.03170920.9970.0150.0350.76799.8
3.29-3.765.10.02270490.9980.0110.0250.7499.7
3.76-4.734.90.02470690.9980.0120.0271.13599.3
4.73-304.70.01972040.9990.0090.0210.898.3

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TMR

4tmr


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.872 / SU B: 9.746 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.43 / ESU R Free: 0.293
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3058 6780 9.8 %RANDOM
Rwork0.2486 ---
obs0.2542 62171 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 85.82 Å2 / Biso mean: 33.124 Å2 / Biso min: 12.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0 Å2-0 Å2
2--0.13 Å2-0 Å2
3----0.31 Å2
Refinement stepCycle: final / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10374 0 164 245 10783
Biso mean--33.43 27.78 -
Num. residues----1326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910734
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210368
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.97314514
X-RAY DIFFRACTIONr_angle_other_deg0.988323886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68951323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08725.247486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.946151911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6751548
X-RAY DIFFRACTIONr_chiral_restr0.080.21611
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212195
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022412
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 381 -
Rwork0.34 3501 -
all-3882 -
obs--74.08 %

+
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