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- PDB-3lx3: Plasmodium vivax 6-pyruvoyltetrahydropterin synthase (PTPS) in co... -

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Basic information

Entry
Database: PDB / ID: 3lx3
TitlePlasmodium vivax 6-pyruvoyltetrahydropterin synthase (PTPS) in complex with xanthopterin
Components6-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
2-amino-1,5-dihydropteridine-4,6-dione / 6-pyruvoyltetrahydropterin synthase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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. / Mueller, N. / Verlinde, C.L.M.J. / Van Voorhis, W.C. / Buckner, F.S. / Fan, E. / Hol, W.G.J. / Merritt, E.A.
History
DepositionFeb 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-pyruvoyl tetrahydrobiopterin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2373
Polymers20,9931
Non-polymers2452
Water3,009167
1
A: 6-pyruvoyl tetrahydrobiopterin synthase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)127,42518
Polymers125,9576
Non-polymers1,46712
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 area14930 Å2
ΔGint-55 kcal/mol
Surface area37690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.358, 131.358, 73.577
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-222-

HOH

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Components

#1: Protein 6-pyruvoyl tetrahydrobiopterin synthase


Mass: 20992.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: noncleavable N-term 6xHis tag
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-XTN / 2-amino-1,5-dihydropteridine-4,6-dione / Xanthopterin


Mass: 179.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5N5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 2 ul 5 mg/ml protein (refolded in SGPP buffer + 0.01 mM Zn2+) mixed with 1 ul 0.1 M sodium acetate (pH 5.2), 24% PEG 3350, 10 mM MgCl2, 1 mM TCEP, 2 mM xanthopterin; cryoprotected by 3 sec ...Details: 2 ul 5 mg/ml protein (refolded in SGPP buffer + 0.01 mM Zn2+) mixed with 1 ul 0.1 M sodium acetate (pH 5.2), 24% PEG 3350, 10 mM MgCl2, 1 mM TCEP, 2 mM xanthopterin; cryoprotected by 3 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: 1.55→50 Å / Num. obs: 35343 / % possible obs: 99.6 % / Observed criterion σ(I): 4 / Redundancy: 9 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.057 / Χ2: 1.045 / Net I/σ(I): 12.8
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3414 / Χ2: 1.128 / % possible all: 96.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0106refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2a0s, A chain

2a0s


Resolution: 1.55→37.12 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0.35 / SU B: 2.076 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.167 1835 5.2 %RANDOM
Rwork0.149 ---
obs0.15 35342 99.55 %-
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: 66.01 Å2 / Biso mean: 25.948 Å2 / Biso min: 13.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0.47 Å20 Å2
2---0.95 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.55→37.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1396 0 14 177 1587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221446
X-RAY DIFFRACTIONr_bond_other_d0.0010.02991
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.9611969
X-RAY DIFFRACTIONr_angle_other_deg0.9393.0012433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4755178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.79524.74478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13915270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.364159
X-RAY DIFFRACTIONr_chiral_restr0.1070.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021602
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02290
X-RAY DIFFRACTIONr_mcbond_it1.7834844
X-RAY DIFFRACTIONr_mcbond_other0.6054333
X-RAY DIFFRACTIONr_mcangle_it2.87161397
X-RAY DIFFRACTIONr_scbond_it3.976602
X-RAY DIFFRACTIONr_scangle_it6.26910564
LS refinement shellResolution: 1.55→1.587 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 133 -
Rwork0.235 2346 -
all-2479 -
obs--94.73 %
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)
14.5891-5.0645-3.18322.41372.51536.634-0.16320.08450.098-0.00860.08510.03210.2262-0.17630.07810.1145-0.00870.05160.0971-0.0070.033211.12634.291718.515
20.145-0.71370.44440.46530.2221.7505-0.0133-0.0631-0.0542-0.06520.09570.05850.0994-0.0475-0.08240.09770.00380.00510.09380.02590.093-12.710318.171130.49
36.184-3.3562-8.95771.06454.109414.4316-0.0643-0.2305-0.25690.0699-0.01720.07040.02450.38240.08150.09710.02310.00210.148800.05331.727910.311925.0406
41.881-0.9136-0.26990.9826-0.20280.6083-0.05090.06570.2557-0.0617-0.067-0.06430.03980.05240.11790.08070.02770.04550.11760.02370.084215.96889.502818.5968
53.8351-4.4261-3.52189.61582.15032.1478-0.0973-0.28930.38480.07680.115-0.09150.05640.3812-0.01770.02820.0240.00240.1109-0.06210.13517.4419.821128.658
61.2609-0.43420.59420.6374-0.26012.17730.097-0.21010.3964-0.1548-0.0761-0.14230.0524-0.0918-0.02090.11230.01140.01950.05360.0180.1034-9.058626.125427.1338
71.62751.31091.44072.39411.24941.7635-0.0078-0.00530.1663-0.1168-0.06570.143-0.0984-0.17510.07350.11160.0055-0.00060.09830.02470.0602-19.434133.276129.3735
80.659-0.6531-0.35771.18430.47170.60670.09310.00180.0906-0.1124-0.0107-0.0625-0.05410.0538-0.08240.10520.00240.01590.07820.02310.0706-6.486623.058722.6086
92.46550.4655-0.96252.0631-1.2125-1.0910.06380.1620.4613-0.0976-0.0637-0.11830.08910.0157-0.00020.05790.03230.05170.07020.08630.108512.266918.28814.0372
102.58780.5771-1.9780.8896-0.31491.67410.0430.08130.1115-0.02410.0330.10510.14690.0371-0.0760.11590.0042-0.00020.11210.01690.0441-2.17610.402619.6234
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 19
2X-RAY DIFFRACTION2A20 - 44
3X-RAY DIFFRACTION3A45 - 49
4X-RAY DIFFRACTION4A50 - 66
5X-RAY DIFFRACTION5A67 - 75
6X-RAY DIFFRACTION6A76 - 88
7X-RAY DIFFRACTION7A89 - 113
8X-RAY DIFFRACTION8A114 - 138
9X-RAY DIFFRACTION9A139 - 151
10X-RAY DIFFRACTION10A152 - 172

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