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- PDB-1b6z: 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1b6z
Title6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE
Components6-pyruvoyl tetrahydropterin synthase
KeywordsLYASE / PTERIN
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, histidine active site / 6-pyruvoyl tetrahydropterin synthase signature 2. / 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
6-pyruvoyl tetrahydrobiopterin synthase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPloom, T. / Thoeny, B. / Yim, J. / Lee, S. / Nar, H. / Leimbacher, W. / Huber, R. / Richardson, J. / Auerbach, G.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystallographic and kinetic investigations on the mechanism of 6-pyruvoyl tetrahydropterin synthase.
Authors: Ploom, T. / Thony, B. / Yim, J. / Lee, S. / Nar, H. / Leimbacher, W. / Richardson, J. / Huber, R. / Auerbach, G.
History
DepositionJan 18, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jan 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 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_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_conn.ptnr2_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8814
Polymers31,7502
Non-polymers1312
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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)95,64312
Polymers95,2516
Non-polymers3926
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area15000 Å2
ΔGint-273 kcal/mol
Surface area34360 Å2
MethodPQS
Unit cell
Length a, b, c (Å)121.500, 121.500, 61.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.349953, 0.936749, -0.005868), (0.936721, 0.349866, -0.012153), (-0.009331, -0.00975, -0.999909)
Vector: 49.39, -34, 58.13)

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Components

#1: Protein 6-pyruvoyl tetrahydropterin synthase / PTPS


Mass: 15875.165 Da / Num. of mol.: 2 / Fragment: PTERIN BINDING DOMAIN / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P27213, EC: 4.6.1.10
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 4.11 Å3/Da / Density % sol: 70.06 %
Crystal growpH: 9.2 / Details: 1.6 M AMMONIUM SULFATE 0.1 M TRIS/HCL, PH 9.2
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
21 mMMes/NaOH1drop
31.3 Mammonium sulfate1reservoir
40.1 MTris-HCl1reservoir
52 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 32839 / % possible obs: 92.6 % / Observed criterion σ(I): 1.7 / Redundancy: 3.4 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066
Reflection
*PLUS
Num. measured all: 111420
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.1 Å / % possible obs: 94.6 % / Rmerge(I) obs: 0.32

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Processing

SoftwareName: X-PLOR / Version: 3.851 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GTQ

1gtq


Resolution: 2→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 1.7
RfactorNum. reflection% reflectionSelection details
Rfree0.256 --RANDOM
Rwork0.216 ---
obs-32839 92.6 %-
Displacement parametersBiso mean: 31.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati sigma a0.33 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 0 2 155 2358
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.89
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.46
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev Biso : 1.38 Å2 / Rms dev position: 0.22 Å / Weight Biso : 1 / Weight position: 25
Software
*PLUS
Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.46
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.1 Å / Rfactor Rfree: 0.342 / Rfactor Rwork: 0.397

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