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- PDB-5gvk: Plasmodium vivax SHMT bound with PLP-glycine and GS256 -

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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


purine nucleobase biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / mRNA regulatory element binding translation repressor activity ...purine nucleobase biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / mRNA regulatory element binding translation repressor activity / cellular response to leukemia inhibitory factor / mRNA 5'-UTR binding / pyridoxal phosphate binding / protein homotetramerization / protein homodimerization activity / zinc ion binding / nucleus / cytosol
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 / Pyridoxal phosphate-dependent transferase ...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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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Phasing

PhasingMethod: molecular replacement

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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 %

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