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- PDB-5xms: Plasmodium vivax SHMT bound with PLP-glycine and GS498 -

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Basic information

Entry
Database: PDB / ID: 5xms
TitlePlasmodium vivax SHMT bound with PLP-glycine and GS498
ComponentsSerine hydroxymethyltransferase
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 / methyltransferase activity / pyridoxal phosphate binding / methylation
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-8B3 / Chem-PLG / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
Model detailsPlasmodium vivax SHMT bound with PLP-glycine and GS362
AuthorsChitnumsub, P. / Jaruwat, A. / Leartsakulpanich, U. / Schwertz, G. / Diederich, F.
Funding support Thailand, 2items
OrganizationGrant numberCountry
National Science and Technology development AgencyCPMO-P-13-00835 Thailand
National Center for Genetic Engineering and BiotechnologyPlatform P-14-50241 Thailand
CitationJournal: Chemistry / Year: 2017
Title: Conformational Aspects in the Design of Inhibitors for Serine Hydroxymethyltransferase (SHMT): Biphenyl, Aryl Sulfonamide, and Aryl Sulfone Motifs
Authors: Schwertz, G. / Frei, M.S. / Witschel, M.C. / Rottmann, M. / Leartsakulpanich, U. / Chitnumsub, P. / Jaruwat, A. / Ittarat, W. / Schafer, A. / Aponte, R.A. / Trapp, N. / Mark, K. / Chaiyen, P. / Diederich, F.
History
DepositionMay 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)150,10611
Polymers147,7473
Non-polymers2,3598
Water5,945330
1
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0597
Polymers98,4982
Non-polymers1,5615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9580 Å2
ΔGint-54 kcal/mol
Surface area29710 Å2
MethodPISA
2
C: Serine hydroxymethyltransferase
hetero molecules

C: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0958
Polymers98,4982
Non-polymers1,5966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9570 Å2
ΔGint-58 kcal/mol
Surface area29770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.808, 58.794, 235.131
Angle α, β, γ (deg.)90.000, 89.990, 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


Mass: 49249.160 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-442
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, UniProt: A5K8L9*PLUS, 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-8B3 / (4~{S})-6-azanyl-4-[3-(2-fluorophenyl)-5-(trifluoromethyl)phenyl]-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazole-5- carbonitrile / (s)-6-amino-4-(2'-fluoro-5-(trifluoromethyl)-[1,1'-biphenyl]-3-yl)-4-isopropyl-3-methyl-2,4-dihydropyrano[2,3-c]pyrazol e-5-carbonitrile


Mass: 456.435 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H20F4N4O
#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.: 330 / 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: 2.38 Å3/Da / Density % sol: 48.35 % / Mosaicity: 0.38 °
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: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 49206 / % possible obs: 95.2 % / Redundancy: 2 % / Rmerge(I) obs: 0.017 / Rpim(I) all: 0.015 / Rrim(I) all: 0.022 / Χ2: 0.767 / Net I/σ(I): 37.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.541.90.0580.9920.0510.0770.91388.7
2.54-2.6420.0450.9950.0390.060.82998
2.64-2.7620.0340.9960.030.0450.82597.9
2.76-2.920.0270.9960.0240.0370.81597.7
2.9-3.0920.0210.9970.0190.0280.77297.3
3.09-3.3220.0170.9980.0150.0230.72996.8
3.32-3.6620.0150.9980.0130.020.71296.2
3.66-4.1920.0140.9980.0120.0180.64995.7
4.19-5.2720.0150.9980.0130.0190.75394.1
5.27-3020.0150.9990.0130.020.69589.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4tmr

4tmr


Resolution: 2.45→30 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.88 / SU B: 11.305 / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.099 / ESU R Free: 0.358
RfactorNum. reflection% reflectionSelection details
Rfree0.2804 4837 9.9 %RANDOM
Rwork0.2179 ---
obs0.2241 44239 95.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 86.52 Å2 / Biso mean: 33.873 Å2 / Biso min: 10.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.03 Å2
2--0.14 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 2.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10374 0 161 330 10865
Biso mean--26.36 30.55 -
Num. residues----1326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910731
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210341
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.97614517
X-RAY DIFFRACTIONr_angle_other_deg1.179323811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.41951323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25425.247486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.149151911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4551548
X-RAY DIFFRACTIONr_chiral_restr0.0850.21611
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212195
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022424
LS refinement shellResolution: 2.45→2.513 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 287 -
Rwork0.29 2871 -
all-3158 -
obs--85.79 %

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