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- PDB-1y13: Structural Analysis of Plasmodium falciparum 6-pyruvoyl tetrahydr... -

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Basic information

Entry
Database: PDB / ID: 1y13
TitleStructural Analysis of Plasmodium falciparum 6-pyruvoyl tetrahydropterin synthase (PTPS)
Components6-pyruvoyl tetrahydropterin synthase
KeywordsLYASE / BIOSYNTHETIC PROTEIN / Structural Genomics of Pathogenic Protozoa Consortium / SGPP / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE
Function / homology
Function and homology information


Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / 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
BIOPTERIN / : / 6-pyruvoyltetrahydropterin synthase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsBosch, J. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be Published
Title: Structural Analysis of Plasmodium falciparum 6-pyruvoyl tetrahydropterin synthase (PTPS)
Authors: Bosch, J. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
History
DepositionNov 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-pyruvoyl tetrahydropterin synthase
B: 6-pyruvoyl tetrahydropterin synthase
C: 6-pyruvoyl tetrahydropterin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4129
Polymers63,5043
Non-polymers9086
Water2,270126
1
A: 6-pyruvoyl tetrahydropterin synthase
B: 6-pyruvoyl tetrahydropterin synthase
C: 6-pyruvoyl tetrahydropterin synthase
hetero molecules

A: 6-pyruvoyl tetrahydropterin synthase
B: 6-pyruvoyl tetrahydropterin synthase
C: 6-pyruvoyl tetrahydropterin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,82318
Polymers127,0076
Non-polymers1,81612
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area20480 Å2
ΔGint-276 kcal/mol
Surface area36000 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)103.319, 103.319, 131.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11C-176-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C
101A
111B
121C
131A
141B
151C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNVALVAL2AA11 - 9019 - 98
21ASNASNVALVAL2BB11 - 9019 - 98
31ASNASNVALVAL2CC11 - 9019 - 98
42LEULEUASNASN4AA91 - 9999 - 107
52LEULEUASNASN4BB91 - 9999 - 107
62LEULEUASNASN4CC91 - 9999 - 107
73ILEILEPROPRO2AA100 - 113108 - 121
83ILEILEPROPRO2BB100 - 113108 - 121
93ILEILEPROPRO2CC100 - 113108 - 121
104GLUGLUASPASP4AA114 - 116122 - 124
114GLUGLUASPASP4BB114 - 116122 - 124
124GLUGLUASPASP4CC114 - 116122 - 124
135CYSCYSBIOBIO2AA - E117 - 175125
145CYSCYSBIOBIO2BB - G117 - 175125
155CYSCYSBIOBIO2CC - I117 - 175125

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Components

#1: Protein 6-pyruvoyl tetrahydropterin synthase / PTPS


Mass: 21167.896 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid details: T7 system / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3)
References: GenBank: 23612358, UniProt: C6KTB6*PLUS, 6-pyruvoyltetrahydropterin synthase
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 237.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H11N5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: PEG 1000, HEPES, Ammonium Chloride - Reservoir: 2.2 M Lithium Chloride, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979029 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 13, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979029 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 36614 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Biso Wilson estimate: 53.55 Å2 / Rsym value: 0.162 / Net I/σ(I): 10.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 5241 / Rsym value: 0.0121 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 11.157 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23481 1847 5.1 %RANDOM
Rwork0.19536 ---
all0.19724 36614 --
obs0.19724 34709 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.965 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3972 0 52 126 4150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224112
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9565552
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4785486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36124.375192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23515739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7411515
X-RAY DIFFRACTIONr_chiral_restr0.0950.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023058
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21709
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22866
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2165
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0710.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.283
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.63262508
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.132103993
X-RAY DIFFRACTIONr_scbond_it5.093101843
X-RAY DIFFRACTIONr_scangle_it6.397151559
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A604tight positional0.050.05
2B604tight positional0.050.05
3C604tight positional0.040.05
1A729medium positional0.550.5
2B729medium positional0.460.5
3C729medium positional0.380.5
1A604tight thermal0.160.5
2B604tight thermal0.150.5
3C604tight thermal0.160.5
1A729medium thermal1.232
2B729medium thermal1.182
3C729medium thermal1.242
LS refinement shellResolution: 2.2→2.317 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.307 270 -
Rwork0.24 4905 -
obs--99.81 %
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)
14.67862.605-1.40921.9248-1.07251.92370.05180.37610.1379-0.08530.18110.0803-0.0589-0.0676-0.2329-0.16810.0527-0.0178-0.07110.0063-0.255469.317415.052920.8863
29.4113-1.57433.68030.88950.0272.4386-0.0213-0.0177-0.7114-0.1590.0616-0.36540.2686-0.0417-0.0403-0.030.08590.0239-0.0803-0.08890.1491.1914-0.852622.3356
36.69170.15763.00911.71050.23944.78620.24440.2258-0.9214-0.1706-0.0395-0.35370.5085-0.2358-0.20490.04540.1030.10330.0066-0.19730.168392.2576-1.159315.3162
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 173
2X-RAY DIFFRACTION2C11 - 81
3X-RAY DIFFRACTION3C123 - 173

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