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- PDB-5gvp: Plasmodium vivax SHMT bound with PLP-glycine and GS654 -

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Basic information

Entry
Database: PDB / ID: 5gvp
TitlePlasmodium vivax SHMT bound with PLP-glycine and GS654
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-GCF / Chem-PLG / glycine hydroxymethyltransferase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.26 Å
Model detailsPlasmodium vivax SHMT bound with PLP-glycine and GS654
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

Downloads & links

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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)150,26911
Polymers147,7473
Non-polymers2,5218
Water4,900272
1
A: Serine hydroxymethyltransferase, putative
B: Serine hydroxymethyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1677
Polymers98,4982
Non-polymers1,6695
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10150 Å2
ΔGint-54 kcal/mol
Surface area29990 Å2
MethodPISA
2
C: Serine hydroxymethyltransferase, putative
hetero molecules

C: Serine hydroxymethyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2038
Polymers98,4982
Non-polymers1,7046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10160 Å2
ΔGint-80 kcal/mol
Surface area29770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.075, 58.928, 234.830
Angle α, β, γ (deg.)90.000, 90.060, 90.000
Int Tables number5
Space group name H-MC121

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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-GCF / 3-[3-[3-[(4~{S})-6-azanyl-5-cyano-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazol-4-yl]-5-(trifluoromethyl)phenyl]phenyl]propanoic acid


Mass: 510.508 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H25F3N4O3
#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.: 272 / 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: 2.39 Å3/Da / Density % sol: 48.54 % / Mosaicity: 0.26 °
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→50.01 Å / Num. obs: 63448 / % possible obs: 96.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.02 / Net I/av σ(I): 51.399 / Net I/σ(I): 32.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.26-2.342.90.1260.982181.8
2.34-2.433.50.0880.99193.1
2.43-2.553.70.0660.995196.6
2.55-2.683.80.0470.996197.9
2.68-2.853.90.0330.997198.8
2.85-3.073.90.0250.998199.4
3.07-3.3840.0190.998199.7
3.38-3.864.10.0170.998199.3
3.86-4.873.90.0210.998199.3
4.87-503.60.0150.999196.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4tmr


Resolution: 2.26→50.01 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.869 / SU B: 10.222 / SU ML: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.527 / ESU R Free: 0.322
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3115 6374 10.1 %RANDOM
Rwork0.2501 ---
obs0.2563 57000 95.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 69.4 Å2 / Biso mean: 29.185 Å2 / Biso min: 6.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.03 Å2
2---0.07 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.26→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10374 0 173 272 10819
Biso mean--24.83 24.62 -
Num. residues----1326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910743
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210353
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.97714535
X-RAY DIFFRACTIONr_angle_other_deg0.998323841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64351323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70825.247486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.848151911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6861548
X-RAY DIFFRACTIONr_chiral_restr0.080.21611
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112222
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022424
X-RAY DIFFRACTIONr_mcbond_it1.5622.8695310
X-RAY DIFFRACTIONr_mcbond_other1.5612.8695311
X-RAY DIFFRACTIONr_mcangle_it2.5324.3016627
LS refinement shellResolution: 2.257→2.316 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 415 -
Rwork0.337 3118 -
all-3533 -
obs--74.22 %

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