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- PDB-5yg1: Plasmodium vivax SHMT bound with PLP-glycine and GS704 -

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Basic information

Entry
Database: PDB / ID: 5yg1
TitlePlasmodium vivax SHMT bound with PLP-glycine and GS704
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE/INHIBITOR / alpha and beta protein / Transferase / methyltransferase activity / Inhibitor / 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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-8UU / 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 GS834
AuthorsChitnumsub, P. / Jaruwat, A. / Leartsakulpanich, U. / Schwertz, G. / Diederich, F.
CitationJournal: to be published
Title: to be published
Authors: Chitnumsub, P. / Jaruwat, A.
History
DepositionSep 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: 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

Downloads & links

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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)150,29011
Polymers147,7473
Non-polymers2,5428
Water3,153175
1
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1817
Polymers98,4982
Non-polymers1,6835
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9810 Å2
ΔGint-54 kcal/mol
Surface area29610 Å2
MethodPISA
2
C: Serine hydroxymethyltransferase
hetero molecules

C: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2178
Polymers98,4982
Non-polymers1,7186
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10040 Å2
ΔGint-78 kcal/mol
Surface area29390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.471, 58.632, 234.636
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number5
Space group name H-MC121

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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-8UU / 3-[1-[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]piperidin-4-yl]propanoic acid


Mass: 517.543 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H30F3N5O3
#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.: 175 / 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: 47.93 % / Mosaicity: 0.51 °
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 14, 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: 49369 / % possible obs: 96 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.016 / Rpim(I) all: 0.011 / Rrim(I) all: 0.02 / Χ2: 0.761 / Net I/σ(I): 30.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.542.30.09245040.9850.0720.1170.73288.7
2.54-2.642.50.06947650.990.050.0860.75394
2.64-2.762.50.05248480.9940.0380.0640.78895.1
2.76-2.92.60.03949460.9950.0280.0480.78196
2.9-3.092.60.02749770.9960.020.0340.73596.7
3.09-3.322.80.0249540.9970.0150.0250.75697.8
3.32-3.6630.01851080.9980.0120.0210.81798.1
3.66-4.193.20.01450740.9980.0090.0170.77298.4
4.19-5.273.20.01550310.9990.0090.0180.89997.6
5.27-303.20.01251620.9990.0080.0140.57497

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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: 0.92 / Cor.coef. Fo:Fc free: 0.867 / SU B: 12.817 / SU ML: 0.286 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.606 / ESU R Free: 0.372
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2942 4840 9.9 %RANDOM
Rwork0.2246 ---
obs0.2315 44275 95.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 95.09 Å2 / Biso mean: 35.504 Å2 / Biso min: 8.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.02 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10374 0 173 175 10722
Biso mean--30.17 26.4 -
Num. residues----1326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910743
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210368
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.97414532
X-RAY DIFFRACTIONr_angle_other_deg1.027323886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.28251323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.33925.247486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.835151911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8181548
X-RAY DIFFRACTIONr_chiral_restr0.080.21614
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212195
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022412
LS refinement shellResolution: 2.45→2.513 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 311 -
Rwork0.301 2912 -
all-3223 -
obs--86.97 %

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