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- PDB-2a0s: Crystal structure of 6-pyruvoyl tetrahydropterin synthase (PTPS) ... -

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Basic information

Entry
Database: PDB / ID: 2a0s
TitleCrystal structure of 6-pyruvoyl tetrahydropterin synthase (PTPS) from Plasmodium vivax at 2.2 A resolution
Components6-pyruvoyl tetrahydropterin synthase
KeywordsLYASE / BIOSYNTHETIC PROTEIN / SGPP / Structural GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / 6-pyruvoyl tetrahydropterin synthase / PTPS / Plasmodium / vivax / Structural Genomics of Pathogenic Protozoa Consortium
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
BIOPTERIN / 6-pyruvoyltetrahydropterin synthase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBosch, J. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be Published
Title: Crystal structure of 6-pyruvoyl tetrahydropterin synthase (PTPS) from Plasmodium vivax at 2.2 A resolution
Authors: Bosch, J. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
History
DepositionJun 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 23, 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_ncs_dom_lim / 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_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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN ZN 281 AND BIO 282 ARE ASSOCIATED WITH PROTEIN CHAIN A ZN 381 AND BIO 382 ARE ASSOCIATED ...HETEROGEN ZN 281 AND BIO 282 ARE ASSOCIATED WITH PROTEIN CHAIN A ZN 381 AND BIO 382 ARE ASSOCIATED WITH PROTEIN CHAIN B
Remark 999SEQUENCE The sequence of this protein is available at PlasmoDB with id Pv_3878.phat_30.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5916
Polymers41,9862
Non-polymers6054
Water3,351186
1
A: 6-pyruvoyl tetrahydropterin synthase
B: 6-pyruvoyl tetrahydropterin synthase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)127,77318
Polymers125,9576
Non-polymers1,81612
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area19660 Å2
ΔGint-255 kcal/mol
Surface area36940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)132.095, 132.095, 74.126
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 2 / Auth seq-ID: 18 - 180 / Label seq-ID: 18 - 180

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein 6-pyruvoyl tetrahydropterin synthase


Mass: 20992.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: MAL6P1.148 / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3)
References: UniProt: A5K2B2, 6-pyruvoyltetrahydropterin synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BIO / BIOPTERIN


Mass: 237.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11N5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 3.1 Å3/Da / Density % sol: 60.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 18% w/v PEG4000, 0.05 M Sodium Acetate pH 4.6 , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 21321 / % possible obs: 91.78 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 33.75 Å2 / Rsym value: 0.06 / Net I/σ(I): 11.9
Reflection shellResolution: 2.2→2.319 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2120 / Rsym value: 0.4 / % possible all: 62.61

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1Y13

1y13


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.533 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.267 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24575 1152 5.1 %RANDOM
Rwork0.20838 ---
all0.21023 ---
obs0.21023 21321 91.78 %-
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: 35.155 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å20 Å2
2---0.26 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 0 36 186 2874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222825
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9051.9653831
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1965342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93524.483145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39815513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.8681517
X-RAY DIFFRACTIONr_chiral_restr0.0570.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022155
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1610.21235
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.21920
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0890.2194
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.2106
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7841734
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34262732
X-RAY DIFFRACTIONr_scbond_it1.10161264
X-RAY DIFFRACTIONr_scangle_it1.835101094
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
661tight positional0.010.05
689medium positional0.160.5
661tight thermal0.010.5
689medium thermal0.12
LS refinement shellResolution: 2.2→2.319 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.304 114 -
Rwork0.267 2120 -
obs--62.61 %
Refinement TLS params.Method: refined / Origin x: -3.429 Å / Origin y: -19.237 Å / Origin z: 0.227 Å
111213212223313233
T-0.0288 Å20.0041 Å20.0127 Å2--0.0411 Å2-0.0011 Å2---0.0356 Å2
L1.8975 °21.6004 °21.0025 °2-1.4749 °20.5848 °2--1.0733 °2
S0.0647 Å °0.0267 Å °-0.1291 Å °0.0948 Å °-0.0026 Å °-0.0777 Å °0.0049 Å °0.0798 Å °-0.062 Å °

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