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- PDB-4pfn: Crystal structure of Plasmodium vivax SHMT with L-serine Schiff base -

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Basic information

Entry
Database: PDB / ID: 4pfn
TitleCrystal structure of Plasmodium vivax SHMT with L-serine Schiff base
ComponentsSerine hydroxymethyltransferase, putative
KeywordsTRANSFERASE / PLP-dependent protein / alpha and beta protein / methyltransferase activity
Function / homology
Function and homology information


purine nucleobase biosynthetic process / serine binding / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / mRNA regulatory element binding translation repressor activity ...purine nucleobase biosynthetic process / serine binding / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / mRNA regulatory element binding translation repressor activity / cellular response to leukemia inhibitory factor / mRNA 5'-UTR binding / pyridoxal phosphate binding / protein homotetramerization / protein homodimerization activity / zinc ion binding / nucleus / cytosol
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 / Pyridoxal phosphate-dependent transferase ...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
PYRIDOXAL-5'-PHOSPHATE / SERINE / glycine hydroxymethyltransferase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
Model detailsX-ray structures of Plasmodium vivax SHMT with L-serine Schiff base
AuthorsChitnumsub, P. / Jaruwat, A. / Leartsakulpanich, U.
Funding support Thailand, 5items
OrganizationGrant numberCountry
Cluster Program and Management Office, National Science and Technology development AgencyCPMO-P-00-20029 Thailand
the Cluster Program and Management Office for Discovery based Development GrantCPMO-DD/P-10-11274 Thailand
Synchron Light Research Institute-Public Organization2-2549/LS01 Thailand
Synchron Light Research Institute-Public Organization2551/08 Thailand
The Thailand Research FundRTA5680001 Thailand
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structures of Plasmodium vivax serine hydroxymethyltransferase: implications for ligand-binding specificity and functional control.
Authors: Chitnumsub, P. / Jaruwat, A. / Riangrungroj, P. / Ittarat, W. / Noytanom, K. / Oonanant, W. / Vanichthanankul, J. / Chuankhayan, P. / Maenpuen, S. / Chen, C.J. / Chaiyen, P. / Yuthavong, Y. ...Authors: Chitnumsub, P. / Jaruwat, A. / Riangrungroj, P. / Ittarat, W. / Noytanom, K. / Oonanant, W. / Vanichthanankul, J. / Chuankhayan, P. / Maenpuen, S. / Chen, C.J. / Chaiyen, P. / Yuthavong, Y. / Leartsakulpanich, U.
History
DepositionApr 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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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)148,87511
Polymers147,7473
Non-polymers1,1288
Water6,864381
1
A: Serine hydroxymethyltransferase, putative
B: Serine hydroxymethyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2387
Polymers98,4982
Non-polymers7405
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10010 Å2
ΔGint-40 kcal/mol
Surface area30390 Å2
MethodPISA
2
C: Serine hydroxymethyltransferase, putative
hetero molecules

C: Serine hydroxymethyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2748
Polymers98,4982
Non-polymers7756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10050 Å2
ΔGint-40 kcal/mol
Surface area30210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.399, 57.940, 235.918
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-503-

CL

DetailsThe biological unit is the same as asymmetric unit

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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
Details: PLP-L-serine external aldimine
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Strain: Salvador I / Gene: PVX_100730 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5K8L9
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7NO3
#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.: 381 / 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: 47.03 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 8.5 / Details: PEG4000, 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 315r / Detector: CCD / Date: Nov 2, 2010 / Details: Rh Coated mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 44633 / % possible obs: 94.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.028 / Χ2: 1.129 / Net I/av σ(I): 38.728 / Net I/σ(I): 33.1 / Num. measured all: 132526
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.592.70.10638210.76482.5
2.59-2.692.80.08540180.82485.1
2.69-2.822.90.06541490.9188.6
2.82-2.962.90.05243371.02691.7
2.96-3.1530.03745301.02695.6
3.15-3.393.10.02847061.06699.3
3.39-3.733.10.02347001.12699.7
3.73-4.273.10.02347311.4199.8
4.27-5.3830.02447461.67799.3
5.38-3030.01848951.20799.2

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4O6Z

4o6z


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.895 / SU B: 10.409 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 4464 10 %RANDOM
Rwork0.207 40169 --
obs0.2126 -93.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 78.68 Å2 / Biso mean: 29.433 Å2 / Biso min: 6.29 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å20 Å20.5 Å2
2--2.78 Å20 Å2
3----5.57 Å2
Refinement stepCycle: final / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10374 0 2 381 10757
Biso mean--25.07 23.71 -
Num. residues----1332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0210629
X-RAY DIFFRACTIONr_angle_refined_deg1.1371.96514355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.58851323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38925.247486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.478151911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6261548
X-RAY DIFFRACTIONr_chiral_restr0.0730.21605
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217962
LS refinement shellResolution: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 267 -
Rwork0.255 2453 -
all-2720 -
obs--80.31 %

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