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- PDB-3m0n: Plasmodium vivax 6-pyruvoyltetrahydropterin synthase (PTPS), E37A... -

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Basic information

Entry
Database: PDB / ID: 3m0n
TitlePlasmodium vivax 6-pyruvoyltetrahydropterin synthase (PTPS), E37A catalytic residue mutant
ComponentsPutative 6-pyruvoyl tetrahydrobiopterin synthase
KeywordsBIOSYNTHETIC PROTEIN / PTS / PTP SYNTHASE / PTPS / METAL-BINDING / TETRAHYDROBIOPTERIN BIOSYNTHESIS / FOLATE BIOSYNTHESIS / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP
Function / homology
Function and homology information


6-pyruvoyltetrahydropterin synthase / 6-pyruvoyltetrahydropterin synthase activity / tetrahydrobiopterin biosynthetic process / metal ion binding
Similarity search - Function
6-pyruvoyl tetrahydropterin synthase/QueD / 6-pyruvoyl tetrahydropterin synthase/QueD family / 6-pyruvoyl tetrahydropterin synthase/QueD superfamily / 6-pyruvoyl tetrahydropterin synthase / Tetrahydropterin Synthase; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PTERINE / 6-pyruvoyltetrahydropterin synthase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsLarson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
CitationJournal: to be published
Title: Structural analysis of the dual-functional 6-pyruvoyltetrahydropterin synthase from Malaria parasites.
Authors: Larson, E.T. / Bosch, J. / Kim, J.E. / Kelley, A. / Castaneda, L. / Napuli, A. / Mueller, N. / Verlinde, C.L.M.J. / Van Voorhis, W.C. / Buckner, F.S. / Fan, E. / Hol, W.G.J. / Merritt, E.A.
History
DepositionMar 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative 6-pyruvoyl tetrahydrobiopterin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1633
Polymers20,9351
Non-polymers2292
Water1,06359
1
A: Putative 6-pyruvoyl tetrahydrobiopterin synthase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)126,98018
Polymers125,6096
Non-polymers1,37112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area15220 Å2
ΔGint-54 kcal/mol
Surface area37920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.750, 131.750, 74.240
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Putative 6-pyruvoyl tetrahydrobiopterin synthase


Mass: 20934.863 Da / Num. of mol.: 1 / Mutation: E37A
Source method: isolated from a genetically manipulated source
Details: E37A mutation confirmed from plasmid DNA sequence
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVX_114505 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5K2B2, 6-pyruvoyltetrahydropterin synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PE0 / PTERINE


Mass: 163.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5N5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsE37A MUTATION CONFIRMED FROM PLASMID DNA SEQUENCE

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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: 2.96 Å3/Da / Density % sol: 58.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 2 ul 25 mg/ml protein (in SGPP buffer) mixed with 2 ul 0.1 M sodium acetate (pH 5.2), 28% PEG 3350, 5 mM DTT; cryoprotected by 5 sec dip in 96 mM sodium acetate (pH 5.2), 24% PEG 3350, 134 ...Details: 2 ul 25 mg/ml protein (in SGPP buffer) mixed with 2 ul 0.1 M sodium acetate (pH 5.2), 28% PEG 3350, 5 mM DTT; cryoprotected by 5 sec dip in 96 mM sodium acetate (pH 5.2), 24% PEG 3350, 134 mM NaCl, 20% glycerol, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 4, 2010
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 19474 / % possible obs: 99.8 % / Observed criterion σ(I): 5 / Redundancy: 9.3 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.079 / Χ2: 1.064 / Net I/σ(I): 12.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1947 / Χ2: 0.98 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0106refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0106phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3lx3, ligand removed and with E37 mutated to A

3lx3


Resolution: 1.9→35.3 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 6.565 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: WITH TLS ADDED. Identity of ligand in active site unknown but clear density for pterine ring of substrate or product present so modeled as such
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1011 5.2 %RANDOM
Rwork0.196 ---
obs0.198 19465 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 108.34 Å2 / Biso mean: 49.913 Å2 / Biso min: 23.57 Å2
Baniso -1Baniso -2Baniso -3
1--2.45 Å2-1.22 Å20 Å2
2---2.45 Å20 Å2
3---3.67 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1364 0 13 62 1439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221411
X-RAY DIFFRACTIONr_bond_other_d0.0010.02962
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9611917
X-RAY DIFFRACTIONr_angle_other_deg0.8063.0012351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2835173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2724.45974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1315256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.495159
X-RAY DIFFRACTIONr_chiral_restr0.0760.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021571
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02287
X-RAY DIFFRACTIONr_mcbond_it1.9764833
X-RAY DIFFRACTIONr_mcbond_other0.6424331
X-RAY DIFFRACTIONr_mcangle_it2.89261368
X-RAY DIFFRACTIONr_scbond_it3.3546578
X-RAY DIFFRACTIONr_scangle_it5.0710543
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 74 -
Rwork0.256 1325 -
all-1399 -
obs--97.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
113.3505-8.7108-12.795110.32788.663827.0511-0.4367-0.34190.4754-0.00360.5694-0.67250.62850.2843-0.13270.19790.06480.0210.2290.02090.2929.53886.098621.9497
23.635-0.01181.35452.16461.10034.42050.0215-0.2872-0.2904-0.23890.01980.09360.1359-0.4025-0.04120.2703-0.0286-0.00980.18630.02550.1344-14.709319.392828.8699
33.9568-2.0145-1.94080.77230.94091.3308-0.05360.13920.0648-0.008-0.0329-0.04410.07430.02990.08650.1960.02440.05610.17590.03860.19245.705311.845824.0919
45.3803-0.5237-0.28413.48841.18880.240.1432-0.1067-0.0282-0.02390.1146-0.641-0.01080.1902-0.25770.19320.01430.01260.2548-0.03080.19110.007822.968429.5249
52.14880.367-0.0760.83650.0591.41460.07190.068-0.1104-0.262-0.1081-0.1057-0.1302-0.21590.03630.25940.0061-0.01240.19630.01830.0567-16.680834.70826.3585
610.22663.73393.76035.0921.97136.3126-0.10670.2630.0642-0.1644-0.05540.33130.0101-0.36920.16210.25370.0113-0.00710.2514-0.00290.0772-23.029230.268230.8115
71.0083-1.3474-0.31453.55151.32721.85420.1575-0.0675-0.145-0.2424-0.0602-0.13830.0130.111-0.09730.20110.00120.02130.16250.02930.1592-7.360924.153524.1311
84.84260.4415-1.13542.683-0.61171.04880.14330.18790.381-0.2637-0.0802-0.1484-0.00610.0332-0.06320.23320.02390.03350.15160.05150.19323.589813.837917.9153
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 21
2X-RAY DIFFRACTION2A22 - 36
3X-RAY DIFFRACTION3A37 - 66
4X-RAY DIFFRACTION4A67 - 85
5X-RAY DIFFRACTION5A86 - 99
6X-RAY DIFFRACTION6A100 - 111
7X-RAY DIFFRACTION7A112 - 136
8X-RAY DIFFRACTION8A137 - 172

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