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- PDB-1b66: 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1b66
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 / tetrahydrobiopterin biosynthetic process / mitochondrion / metal ion binding / identical protein 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
BIOPTERIN / 6-pyruvoyl tetrahydrobiopterin synthase
Similarity search - Component
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 20, 1999Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)32,3566
Polymers31,7502
Non-polymers6054
Water4,666259
1
A: 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE
hetero molecules

A: 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE
hetero molecules

A: 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE
hetero molecules

B: 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE
hetero molecules

B: 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE
hetero molecules

B: 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,06718
Polymers95,2516
Non-polymers1,81612
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
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_654-y+1,x-y,z-11
crystal symmetry operation3_664-x+y+1,-x+1,z-11
MethodPQS
2
A: 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE
hetero molecules

A: 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE
hetero molecules

A: 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5339
Polymers47,6253
Non-polymers9086
Water543
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 area7070 Å2
ΔGint-116 kcal/mol
Surface area18910 Å2
MethodPISA
3
B: 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE
hetero molecules

B: 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE
hetero molecules

B: 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5339
Polymers47,6253
Non-polymers9086
Water543
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 area7090 Å2
ΔGint-118 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.270, 120.270, 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: (-0.383926, 0.923363, -0.001366), (0.923357, 0.383917, -0.004499), (-0.00363, -0.002989, -0.999989)
Vector: 51.28, -34.09, 57.8)

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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: 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.: 259 / 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: 4.03 Å3/Da / Density % sol: 69.45 %
Crystal growpH: 9.2 / Details: 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
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 40302 / % possible obs: 99.5 % / Observed criterion σ(I): 1.7 / Redundancy: 3.9 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087
Reflection
*PLUS
Lowest resolution: 28 Å / Num. measured all: 156350
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 97.7 % / Rmerge(I) obs: 0.413

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GTQ

1gtq


Resolution: 1.9→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
Rfree0.258 --RANDOM
Rwork0.227 ---
obs0.227 39982 99.5 %-
Displacement parametersBiso mean: 22.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati sigma a0.33 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2202 0 36 259 2497
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 : 1.14 Å2 / Rms dev position: 0.16 Å / Weight Biso : 1 / Weight position: 25
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 28 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.49
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / Rfactor Rfree: 0.338 / Rfactor obs: 0.329

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