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- PDB-5xmu: Plasmodium vivax SHMT bound with PLP-glycine and GS363 -

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Basic information

Entry
Database: PDB / ID: 5xmu
TitlePlasmodium vivax SHMT bound with PLP-glycine and GS363
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-8A0 / Chem-PLG / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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 / 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
B: Serine hydroxymethyltransferase
C: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,09411
Polymers147,7473
Non-polymers2,3478
Water4,918273
1
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0517
Polymers98,4982
Non-polymers1,5535
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9710 Å2
ΔGint-53 kcal/mol
Surface area29610 Å2
MethodPISA
2
C: Serine hydroxymethyltransferase
hetero molecules

C: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0878
Polymers98,4982
Non-polymers1,5886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9760 Å2
ΔGint-54 kcal/mol
Surface area29520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.534, 58.618, 233.875
Angle α, β, γ (deg.)90.000, 90.040, 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
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-8A0 / (4~{S})-6-azanyl-3-methyl-4-[3-(2-methylphenyl)-5-(trifluoromethyl)phenyl]-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazole-5-carbonitrile / (s)-6-amino-4-isopropyl-3 methyl-4-(2'-methyl-5-(trifluoromethyl)-[1,1'-biphenyl]-3-yl)-2,4-dihydropyrano[2,3-c]pyrazole-5-carbonitrile


Mass: 452.472 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H23F3N4O
#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.: 273 / 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: 2.36 Å3/Da / Density % sol: 47.78 % / Mosaicity: 0.559 °
Crystal growTemperature: 298 K / Method: microbatch / pH: 8.5 / Details: PEG 4000, 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: Aug 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→30 Å / Num. obs: 51273 / % possible obs: 92.2 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.02 / Rrim(I) all: 0.034 / Χ2: 0.836 / Net I/σ(I): 20.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.39-2.482.20.2150.9310.1650.2720.57388.6
2.48-2.572.30.1590.9590.1210.2010.62393.6
2.57-2.692.30.1240.9720.0940.1570.79893.7
2.69-2.832.30.0880.9850.0660.1110.99393.7
2.83-3.012.20.0680.990.0510.0851.14293.6
3.01-3.242.20.0460.9950.0340.0581.22693.5
3.24-3.572.20.0340.9970.0250.0421.15892.7
3.57-4.082.20.0250.9970.0190.0320.85591.9
4.08-5.142.20.0220.9980.0170.0280.69190.6
5.14-302.50.0160.9990.0110.0190.40190.3

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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: 2.39→30 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.857 / SU B: 13.038 / SU ML: 0.297 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.43 / ESU R Free: 0.398
RfactorNum. reflection% reflectionSelection details
Rfree0.3182 5247 10.4 %RANDOM
Rwork0.2321 ---
obs0.2408 45091 91.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 102.32 Å2 / Biso mean: 37.689 Å2 / Biso min: 9.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20.02 Å2
2--0.11 Å2-0 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 2.39→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10374 0 161 273 10808
Biso mean--29.37 31.03 -
Num. residues----1326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910731
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210350
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9714517
X-RAY DIFFRACTIONr_angle_other_deg1.012323829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.93151323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48125.247486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.648151911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8441548
X-RAY DIFFRACTIONr_chiral_restr0.0810.21611
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212195
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022424
LS refinement shellResolution: 2.39→2.452 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 318 -
Rwork0.307 2935 -
all-3253 -
obs--80.64 %

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