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- PDB-2g64: Structure of Caenorhabditis elegans 6-pyruvoyl tetrahydropterin s... -

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Basic information

Entry
Database: PDB / ID: 2g64
TitleStructure of Caenorhabditis elegans 6-pyruvoyl tetrahydropterin synthase
ComponentsPutative 6-pyruvoyl tetrahydrobiopterin synthase
KeywordsLYASE / TETRAHYDROBIOPTERIN BIOSYNTHESIS / PHOSPHATE ELIMINATION / PTERINE SYNTHESIS / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / 6-pyruvoyltetrahydropterin synthase / 6-pyruvoyltetrahydropterin synthase activity / tetrahydrobiopterin biosynthetic process / mitochondrion / identical protein binding / metal ion binding
Similarity search - Function
6-pyruvoyl tetrahydropterin synthase, cysteine active site / 6-pyruvoyl tetrahydropterin synthase signature 1. / 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
Putative 6-pyruvoyl tetrahydrobiopterin synthase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWengerter, B.C. / Patskovsky, Y. / Zhan, C. / Ramagopal, U. / Milstein, S. / Vidal, M. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Caenorhabditis Elegans 6-Pyruvoyl Tetrahydropterin Synthase
Authors: Wengerter, B.C. / Patskovsky, Y. / Zhan, C. / Ramagopal, U. / Milstein, S. / Vidal, M. / Almo, S.C.
History
DepositionFeb 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,2595
Polymers16,0551
Non-polymers2034
Water3,009167
1
A: Putative 6-pyruvoyl tetrahydrobiopterin synthase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)97,55330
Polymers96,3326
Non-polymers1,22124
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_456y-1/3,x+1/3,-z+4/31
crystal symmetry operation11_566x-y+2/3,-y+4/3,-z+4/31
crystal symmetry operation12_556-x+2/3,-x+y+1/3,-z+4/31
Buried area14840 Å2
ΔGint-352 kcal/mol
Surface area37860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.792, 69.792, 160.188
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Putative 6-pyruvoyl tetrahydrobiopterin synthase / PTPS / PTP synthase


Mass: 16055.360 Da / Num. of mol.: 1 / Mutation: C140S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: B0041.6 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 AI
References: UniProt: O02058, 6-pyruvoyltetrahydropterin synthase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 MM HEPES, 1 M SODIUM SUCCINATE, PH 7.00, 1% PEG 2000ME, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 31, 2006 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 14091 / Num. obs: 14091 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rmerge(I) obs: 0.031 / Rsym value: 0.03 / Net I/σ(I): 38.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 14.6 / Num. unique all: 1380 / Rsym value: 0.103 / % possible all: 97.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B66

1b66


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.541 / SU ML: 0.081 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21902 442 3.1 %RANDOM
Rwork0.16058 ---
all0.163 13641 --
obs0.16238 13641 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.347 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.05 Å20 Å2
2--0.11 Å20 Å2
3----0.16 Å2
Refine analyzeLuzzati coordinate error obs: 0.171 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1124 0 9 167 1300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221226
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.9651666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2275163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92324.3453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94415246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.58156
X-RAY DIFFRACTIONr_chiral_restr0.1130.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02903
X-RAY DIFFRACTIONr_nbd_refined0.2320.3560
X-RAY DIFFRACTIONr_nbtor_refined0.310.5833
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.5233
X-RAY DIFFRACTIONr_metal_ion_refined0.1930.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.389
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.280.533
X-RAY DIFFRACTIONr_mcbond_it4.1362737
X-RAY DIFFRACTIONr_mcangle_it5.34631217
X-RAY DIFFRACTIONr_scbond_it9.1723499
X-RAY DIFFRACTIONr_scangle_it10.8775436
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 30 -
Rwork0.208 981 -
obs-981 97.4 %

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