SAXSdb — 1b6z

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1. Protein Identity and Related Structures Protein Identity & Related Structures

6-pyruvoyl tetrahydropterin synthase

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 5–144 Chain B； UniProt 5–144	Fragment：PTERIN BINDING DOMAIN	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 9.2；1.6 M AMMONIUM SULFATE 0.1 M TRIS/HCL, PH 9.2	Resolution 2.00 Å R-free 0.256
2	Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 5–144 Chain B； UniProt 5–144	Fragment：PTERIN BINDING DOMAIN	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：pH 9.2；1.6 M AMMONIUM SULFATE 0.1 M TRIS/HCL, PH 9.2	Resolution 2.00 Å R-free 0.256

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1B6Z	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B66 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE Deposited 1999-01-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 5–144（140 aa） Chain B 5–144（140 aa）	Not recorded	ZN ZINC ION × 6 BIO BIOPTERIN × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 9.2；pH 9.2	Resolution 1.90 Å R-free 0.258
1B66 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE Deposited 1999-01-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 5–144（140 aa）	Not recorded	ZN ZINC ION × 3 BIO BIOPTERIN × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 9.2；pH 9.2	Resolution 1.90 Å R-free 0.258
1B66 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE Deposited 1999-01-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 5–144（140 aa）	Not recorded	ZN ZINC ION × 3 BIO BIOPTERIN × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 9.2；pH 9.2	Resolution 1.90 Å R-free 0.258
1GTQ 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE Deposited 1995-09-16	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 5–144（140 aa） Chain B 5–144（140 aa）	Not recorded	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；pH 9.0	Resolution 2.30 Å

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PTPS_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–140； UniProt 5–144 Author chain B； PDBConstruct 1–140； UniProt 5–144

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1b6z
Deposition date deposition_date	1999-01-18
Structure title title	6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE
Keywords keywords	PTERIN, LYASE; LYASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.25 Å
Radius of gyration Rg (electron density) rg_electron	26.37 Å
Forward intensity I(0) i0	17116200.00
Molecular weight molecular_weight	31488.0 kDa
Excluded volume excluded_volume	39413 Å³
Envelope volume envelope_volume	52880 Å³
Hydration-shell volume shell_volume	18417 Å³
Envelope diameter envelope_diameter	94.3 Å
Shell Rg shell_rg	30.83 Å
Envelope Rg envelope_rg	26.26 Å
Shape Rg shape_rg	26.39 Å
Total Rg total_rg	26.85 Å
Total atoms total_atoms	2202
Residues n_residues	275
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	90.5 Å
Rg (real space) rg_real	27.58 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	1.7120e+07
I(0) uncertainty (real space) i0_real_error	2.7990e+05
Rg (reciprocal space) rg_reciprocal	27.48 Å
I(0) (reciprocal space) i0_reciprocal	17110000.0000
Solution quality estimate total_estimate	0.8387
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.489
Kurtosis Kurtosis kurtosis	-0.512
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2204000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.805; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.608; Smooth: 0.876

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1b6za_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.2 — 6-pyruvoyl tetrahydropterin synthase

Domain ID domain_id	d1b6zb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.2 — 6-pyruvoyl tetrahydropterin synthase

CATH v4.4 (2 domains)

Domain ID domain_id	1b6zA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	479 — Tetrahydropterin Synthase; Chain A
Homologous superfamily homologous superfamily	10 — 6-pyruvoyl tetrahydropterin synthase/QueD

Domain ID domain_id	1b6zB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	479 — Tetrahydropterin Synthase; Chain A
Homologous superfamily homologous superfamily	10 — 6-pyruvoyl tetrahydropterin synthase/QueD

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8. Citations (1)

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Unit-cell length a length_a	121.500 Å
Unit-cell length b length_b	121.500 Å
Unit-cell length c length_c	61.250 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 3 2 1
Space-group number int_tables_number	150
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2160
R_free r_free	0.2560

Description description	6-pyruvoyl tetrahydropterin synthase
Molecular weight formula_weight	15875.2 kDa
EC 编号 ec_number	4.6.1.10
Source method src_method	nat
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2358

6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE

1. Protein Identity and Related Structures Protein Identity & Related Structures

6-pyruvoyl tetrahydropterin synthase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	155

fit	/app/data/saxs_computation/b6/1b6z/1b6z.fit
pddf	/app/data/pr_computation/b6/1b6z/1b6z.pr.out
profile	/app/data/saxs_computation/b6/1b6z/1b6z.dat