[English] 日本語
Yorodumi
- PDB-5gvk: Plasmodium vivax SHMT bound with PLP-glycine and GS256 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gvk
TitlePlasmodium vivax SHMT bound with PLP-glycine and GS256
ComponentsSerine hydroxymethyltransferase, putative
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / alpha and beta protein / methyltransferase activity / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / pyridoxal phosphate binding
Similarity search - Function
: / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...: / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-G45 / Chem-PLG / glycine hydroxymethyltransferase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.24 Å
Model detailsPlasmodium vivax SHMT bound with PLP-glycine and GS256
AuthorsChitnumsub, P. / Jaruwat, A. / Leartsakulpanich, U. / Schwertz, G.
Funding support Thailand, 1items
OrganizationGrant numberCountry
National Science and Technology Development Agency Thailand
CitationJournal: J. Med. Chem. / Year: 2017
Title: Antimalarial Inhibitors Targeting Serine Hydroxymethyltransferase (SHMT) with in Vivo Efficacy and Analysis of their Binding Mode Based on X-ray Cocrystal Structures
Authors: Schwertz, G. / Witschel, M.C. / Rottmann, M. / Bonnert, R. / Leartsakulpanich, U. / Chitnumsub, P. / Jaruwat, A. / Ittarat, W. / Schafer, A. / Aponte, R.A. / Charman, S.A. / White, K.L. / ...Authors: Schwertz, G. / Witschel, M.C. / Rottmann, M. / Bonnert, R. / Leartsakulpanich, U. / Chitnumsub, P. / Jaruwat, A. / Ittarat, W. / Schafer, A. / Aponte, R.A. / Charman, S.A. / White, K.L. / Kundu, A. / Sadhukhan, S. / Lloyd, M. / Freiberg, G.M. / Srikumaran, M. / Siggel, M. / Zwyssig, A. / Chaiyen, P. / Diederich, F.
History
DepositionSep 6, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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, putative
B: Serine hydroxymethyltransferase, putative
C: Serine hydroxymethyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,26311
Polymers147,7473
Non-polymers2,5158
Water7,044391
1
A: Serine hydroxymethyltransferase, putative
B: Serine hydroxymethyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1637
Polymers98,4982
Non-polymers1,6655
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9790 Å2
ΔGint-56 kcal/mol
Surface area29690 Å2
MethodPISA
2
C: Serine hydroxymethyltransferase, putative
hetero molecules

C: Serine hydroxymethyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1998
Polymers98,4982
Non-polymers1,7016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10210 Å2
ΔGint-81 kcal/mol
Surface area29410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.943, 58.297, 233.613
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-503-

CL

-
Components

#1: Protein Serine hydroxymethyltransferase, putative


Mass: 49249.160 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (strain Salvador I) (eukaryote)
Strain: Salvador I / Gene: PVX_100730 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A5K8L9
#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-G45 / 5-[3-[(4~{S})-6-azanyl-5-cyano-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazol-4-yl]-5-cyano-phenyl]-~{N},~{N}-dimethyl-thiophene-2-sulfonamide


Mass: 508.616 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H24N6O3S2
#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.: 391 / 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: 2.33 Å3/Da / Density % sol: 47.12 % / Mosaicity: 0.373 °
Crystal growTemperature: 298 K / Method: microbatch / pH: 8.5 / Details: PEG4000, 0.06-0.12M NaCl, 0.1M Tris-HCl pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.24→30 Å / Num. obs: 62386 / % possible obs: 95.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.057 / Net I/av σ(I): 20.291 / Net I/σ(I): 13.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.25-2.333.60.3530.906180.3
2.33-2.423.80.3080.919188.8
2.42-2.533.90.2480.951195.6
2.53-2.6740.1990.957197.6
2.67-2.834.10.1410.979198.6
2.83-3.054.10.1070.988198.8
3.05-3.364.30.0750.995199.2
3.36-3.854.50.0510.997199.7
3.85-4.844.40.0430.997199.6
4.84-304.40.0270.999199.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TMR

4tmr


Resolution: 2.24→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.904 / SU B: 12.153 / SU ML: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.478 / ESU R Free: 0.305
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2926 6303 10.1 %RANDOM
Rwork0.2152 ---
obs0.2229 56081 95.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 120 Å2 / Biso mean: 48.311 Å2 / Biso min: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å20 Å20.1 Å2
2--2.02 Å2-0 Å2
3----4.22 Å2
Refinement stepCycle: final / Resolution: 2.24→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10374 0 167 391 10932
Biso mean--46.32 43.93 -
Num. residues----1326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910737
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.97314526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70351323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07425.247486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.597151911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4571548
X-RAY DIFFRACTIONr_chiral_restr0.0960.21611
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218058
X-RAY DIFFRACTIONr_mcbond_it2.834.7235310
X-RAY DIFFRACTIONr_mcangle_it4.3427.0766627
X-RAY DIFFRACTIONr_scbond_it3.1274.9335427
LS refinement shellResolution: 2.245→2.303 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 351 -
Rwork0.315 3231 -
all-3582 -
obs--75.78 %

+
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