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

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Basic information

Entry
Database: PDB / ID: 1gtq
Title6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE
Components6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE
KeywordsTETRAHYDROBIOPTERIN BIOSYNTHESIS / PHOSPHATE ELIMINATION / PTERINE SYNTHESIS
Function / homology
Function and homology information


Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / 6-pyruvoyltetrahydropterin synthase / 6-pyruvoyltetrahydropterin synthase activity / 6-carboxy-5,6,7,8-tetrahydropterin 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 rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsNar, H. / Huber, R. / Heizmann, C.W. / Thoeny, B. / Buergisser, D.
CitationJournal: EMBO J. / Year: 1994
Title: Three-dimensional structure of 6-pyruvoyl tetrahydropterin synthase, an enzyme involved in tetrahydrobiopterin biosynthesis.
Authors: Nar, H. / Huber, R. / Heizmann, C.W. / Thony, B. / Burgisser, D.
History
DepositionSep 16, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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.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
Water1,44180
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)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
Unit cell
Length a, b, c (Å)122.300, 122.300, 61.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE


Mass: 15875.165 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / Organ: LIVER / Production host: Escherichia coli (E. coli) / 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


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.19 Å3/Da / Density % sol: 70.62 %
Crystal growpH: 9 / Details: pH 9.0
Crystal
*PLUS
Density % sol: 70 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlprotein1drop
21 mMMES1drop
31 mM1dropNaOH
41.3 Mammonium sulfate1reservoir
50.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceWavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→21.2 Å / Num. obs: 22612 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.116
Reflection
*PLUS
Rmerge(I) obs: 0.116

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.3→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.204 --
obs0.204 21405 93.2 %
Displacement parametersBiso mean: 15.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.01 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 2 240 2942
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.69
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.39
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.39
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.46

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