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- PDB-3lze: Plasmodium vivax 6-pyruvoyltetrahydropterin synthase (PTPS), E37C... -

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Basic information

Entry
Database: PDB / ID: 3lze
TitlePlasmodium vivax 6-pyruvoyltetrahydropterin synthase (PTPS), E37C 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 1, 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 / pdbx_struct_special_symmetry / 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)21,1953
Polymers20,9671
Non-polymers2292
Water97354
1
A: Putative 6-pyruvoyl tetrahydrobiopterin synthase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)127,17318
Polymers125,8026
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 area15390 Å2
ΔGint-55 kcal/mol
Surface area37720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.495, 131.495, 73.670
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-226-

HOH

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Components

#1: Protein Putative 6-pyruvoyl tetrahydrobiopterin synthase


Mass: 20966.928 Da / Num. of mol.: 1 / Mutation: E37C
Source method: isolated from a genetically manipulated source
Details: E37C 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.: 54 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsE37C 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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 2 ul 17 mg/ml protein (in SGPP buffer) mixed with 1 ul 0.1 M sodium acetate (pH 5.2), 24% PEG 3350, 1 mM TCEP; cryoprotected by 5 sec dip in 96 mM sodium acetate (pH 5.2), 24% PEG 3350, 134 ...Details: 2 ul 17 mg/ml protein (in SGPP buffer) mixed with 1 ul 0.1 M sodium acetate (pH 5.2), 24% PEG 3350, 1 mM TCEP; 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: Jun 18, 2009
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→30 Å / Num. obs: 19289 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 9.2 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.077 / Χ2: 1.044 / Net I/σ(I): 14.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1896 / Χ2: 0.978 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0106refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0106phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3lx3 with mutation and without ligand

3lx3


Resolution: 1.9→29.03 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 6.364 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1005 5.2 %RANDOM
Rwork0.191 ---
obs0.193 19289 99.85 %-
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: 121.2 Å2 / Biso mean: 49.531 Å2 / Biso min: 24 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å2-0.9 Å20 Å2
2---1.81 Å20 Å2
3---2.71 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 0 13 57 1444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221422
X-RAY DIFFRACTIONr_bond_other_d0.0030.02970
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9611933
X-RAY DIFFRACTIONr_angle_other_deg0.8623.0012372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4175175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70324.53375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.515259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.421159
X-RAY DIFFRACTIONr_chiral_restr0.0960.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021589
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02289
X-RAY DIFFRACTIONr_mcbond_it2.7754839
X-RAY DIFFRACTIONr_mcbond_other0.964333
X-RAY DIFFRACTIONr_mcangle_it4.02561380
X-RAY DIFFRACTIONr_scbond_it4.76583
X-RAY DIFFRACTIONr_scangle_it6.61310547
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 74 -
Rwork0.228 1322 -
all-1396 -
obs--99.5 %
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)
112.9164-14.4825-9.79999.43957.180117.9805-0.3609-0.28160.7219-0.12560.4532-1.02710.4643-0.1838-0.09230.15390.07990.06540.19250.02260.25719.5096.02221.8
21.80950.70580.14330.14821.68694.50820.1053-0.3152-0.3074-0.2746-0.0196-0.09360.1972-0.5335-0.08570.2624-0.0289-0.03230.16960.04440.1647-15.1319.27928.598
32.5009-1.0233-1.21570.53680.51060.9516-0.04380.1085-0.0367-0.0693-0.0803-0.02610.09320.01850.12410.18910.03580.05510.1790.06020.18214.55311.323.499
413.6624-12.3732-6.876212.48528.25684.1123-0.0498-0.56430.5393-0.22580.2014-0.5124-0.09260.0783-0.15160.05680.0737-0.00310.1953-0.04740.350910.13817.26226.897
51.67391.60381.03151.86850.45364.16880.1536-0.20870.258-0.1056-0.1154-0.28950.10830.1486-0.03810.2294-0.00010.02530.19190.00070.1775-6.01825.62130.145
60.529-0.1993-0.91751.1850.20632.22260.05940.10570.0107-0.1544-0.1583-0.0481-0.061-0.38170.09890.2746-0.0019-0.02170.24760.01950.0339-19.50332.69728.155
70.7101-1.6295-0.36063.84141.14211.69050.2132-0.1767-0.1279-0.3172-0.0716-0.0787-0.04620.1334-0.14160.2102-0.00360.01470.14280.03120.163-7.28724.1223.945
84.50150.2673-1.70522.6281-0.9270.61680.13350.17090.2561-0.2614-0.2012-0.22040.0933-0.03370.06770.21580.04450.04620.14650.06490.20063.61413.78817.723
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 21
2X-RAY DIFFRACTION2A22 - 37
3X-RAY DIFFRACTION3A38 - 61
4X-RAY DIFFRACTION4A62 - 74
5X-RAY DIFFRACTION5A75 - 85
6X-RAY DIFFRACTION6A86 - 111
7X-RAY DIFFRACTION7A112 - 136
8X-RAY DIFFRACTION8A137 - 172

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