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- PDB-5xmp: Plasmodium vivax SHMT(C346A) bound with PLP-glycine and MF057 -

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Basic information

Entry
Database: PDB / ID: 5xmp
TitlePlasmodium vivax SHMT(C346A) bound with PLP-glycine and MF057
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 / mitochondrion
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-8A3 / Chem-PLG / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
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
B: Serine hydroxymethyltransferase
C: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,48211
Polymers147,6513
Non-polymers2,8308
Water6,035335
1
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3097
Polymers98,4342
Non-polymers1,8755
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-52 kcal/mol
Surface area29750 Å2
MethodPISA
2
C: Serine hydroxymethyltransferase
hetero molecules

C: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3458
Polymers98,4342
Non-polymers1,9106
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area9910 Å2
ΔGint-77 kcal/mol
Surface area29560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.486, 58.089, 234.749
Angle α, β, γ (deg.)90.000, 90.050, 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: 49217.098 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-442 / Mutation: C364A
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-8A3 / 4-[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]-~{N}-methyl-~{N}-[2,2,2-tris(fluoranyl)ethyl]benzenesulfonamide / (s)-3'-(6-amino-5-cyano-4-isopropyl-3-methyl-2,4-dihydropyrano[2,3-c]pyrazol-4-yl)-N-methyl-N-(2,2,2-trifluoroethyl)-5'-(trifluoromethyl)-[1,1'-biphenyl]-4-sulfonamide


Mass: 613.575 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H25F6N5O3S
#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.: 335 / 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: 2.32 Å3/Da / Density % sol: 46.98 % / Mosaicity: 0.721 °
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: 2.4→30 Å / Num. obs: 51013 / % possible obs: 94.2 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.019 / Rpim(I) all: 0.014 / Rrim(I) all: 0.024 / Χ2: 0.756 / Net I/σ(I): 31.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.491.90.0730.9920.0630.0970.7484
2.49-2.592.20.0670.9930.0540.0860.82297
2.59-2.72.20.0510.9940.0410.0660.80898.4
2.7-2.852.20.0380.9960.0310.0490.86198.2
2.85-3.022.20.030.9970.0240.0380.82897.5
3.02-3.262.30.0230.9980.0180.030.78496.5
3.26-3.582.30.0190.9980.0150.0250.77794.8
3.58-4.12.40.0180.9980.0140.0230.77392.7
4.1-5.162.50.0190.9980.0140.0240.79891.5
5.16-302.80.0150.9990.0110.0180.47892

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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: 2.4→30 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.859 / SU B: 12.736 / SU ML: 0.293 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.674 / ESU R Free: 0.384
RfactorNum. reflection% reflectionSelection details
Rfree0.3091 5104 10.1 %RANDOM
Rwork0.2669 ---
obs0.2711 45356 94.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 69.6 Å2 / Biso mean: 32.68 Å2 / Biso min: 10.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0.08 Å2
2--0.02 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10371 0 188 335 10894
Biso mean--37.31 31.13 -
Num. residues----1326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910755
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210359
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9814565
X-RAY DIFFRACTIONr_angle_other_deg0.979323847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91451323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.11625.247486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.589151908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8571548
X-RAY DIFFRACTIONr_chiral_restr0.0770.21620
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112201
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022418
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 385 -
Rwork0.327 2842 -
all-3227 -
obs--84.12 %

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