SAXSdb — 1dbr

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

HYPOXANTHINE GUANINE XANTHINE PHOSPHORIBOSYLTRANSFERASE

Toxoplasma gondii

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–230 Chain B； UniProt 1–230 Chain C； UniProt 1–230 Chain D； UniProt 1–230	Not recorded	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.40 Å

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 1DBR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FSG TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE COMPLEXED WITH 9-DEAZAGUANINE, ALPHA-D-5-PHOSPHORIBOSYL-1-PYROPHOSPHATE (PRPP) AND TWO MG2+ IONS Deposited 2000-09-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–230（230 aa） Chain C 1–230（230 aa）	Not recorded	MG MAGNESIUM ION × 8 PRP 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose × 4 9DG 9-DEAZAGUANINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；THE PROTEIN (20 mg ml-1) WAS MIXED WITH A SOLUTION CONSISTING OF 30% PEG 4000, 100 MM TRIS.HCL (PH 8.0), 200 MM LI2SO4, and 0.5 % BETA-OCTYLGLUCOPYRANOSIDE. THE CRYSTAL WAS GROWN IN THE PRESENCE OF 2 MM 9-DEAZAGUANINE, 2 MM PRPP AND 10 MM MGCL2 AT 277 K. THE CRYSTAL GREW IN 2 DAYS., VAPOR DIFFUSION, HANGING DROP	Resolution 1.05 Å R-free 0.154
1QK3 TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE GMP COMPLEX Deposited 1999-07-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–230（230 aa） Chain B 1–230（230 aa） Chain C 1–230（230 aa） Chain D 1–230（230 aa）	Not recorded	5GP GUANOSINE-5'-MONOPHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；277 K；15% PEG 8000, 100 MM KPO4 (PH 5-6), 0.25% BETA-OCTYLGLUCOPYRANOSIDE, 1 MM GMP, 277 K	Resolution 1.65 Å R-free 0.231
1QK4 TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE IMP COMPLEX Deposited 1999-07-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–230（230 aa） Chain B 1–230（230 aa） Chain C 1–230（230 aa） Chain D 1–230（230 aa）	Not recorded	IMP INOSINIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；277 K；30% PEG 4000, 100 MM TRIS (PH 8.5), 200 MM LI2SO4, 0.25 % BETA-OCTYLGLUCOPYRANOSIDE 1 MM IMP, 277 K	Resolution 1.90 Å R-free 0.238
1QK5 TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE WITH XMP, PYROPHOSPHATE AND TWO MG2+ IONS Deposited 1999-07-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–230（230 aa） Chain B 1–230（230 aa）	Mutation：YES Mutation：YES	XMP XANTHOSINE-5'-MONOPHOSPHATE × 4 POP PYROPHOSPHATE 2- × 4 MG MAGNESIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；277 K；30% PEG 4000, 100 MM TRIS.CL (PH 8.5), 200 MM LI2SO4, 0.25 % BETA-OCTYLGLUCOPYRANOSIDE. THE CRYSTAL WAS GROWN IN THE PRESENCE OF 1 MM XANTHINE, 1 MM PRPP AND 10 MM MGCL2 AT 277 K.	Resolution 1.60 Å R-free 0.261

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

View Construct and Data Evidence

UniProt name	HGXR_TOXGO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–230； UniProt 1–230 Author chain B； PDBConstruct 1–230； UniProt 1–230 Author chain C； PDBConstruct 1–230； UniProt 1–230 Author chain D； PDBConstruct 1–230； UniProt 1–230

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	1dbr
Deposition date deposition_date	1996-02-13
Structure title title	HYPOXANTHINE GUANINE XANTHINE
Keywords keywords	TRANSFERASE, GLYCOSYLTRANSFERASE, PURINE SALVAGE; TRANSFERASE
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	29.15 Å
Radius of gyration Rg (electron density) rg_electron	27.75 Å
Forward intensity I(0) i0	150585000.00
Molecular weight molecular_weight	100650.0 kDa
Excluded volume excluded_volume	127440 Å³
Envelope volume envelope_volume	157310 Å³
Hydration-shell volume shell_volume	44737 Å³
Envelope diameter envelope_diameter	91.8 Å
Shell Rg shell_rg	37.18 Å
Envelope Rg envelope_rg	27.88 Å
Shape Rg shape_rg	27.73 Å
Total Rg total_rg	28.78 Å
Total atoms total_atoms	7107
Residues n_residues	876
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	87.5 Å
Rg (real space) rg_real	28.97 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	1.5060e+08
I(0) uncertainty (real space) i0_real_error	2.2540e+06
Rg (reciprocal space) rg_reciprocal	29.05 Å
I(0) (reciprocal space) i0_reciprocal	150600000.0000
Solution quality estimate total_estimate	0.9017
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.9 Å
Skewness Skewness skewness	0.130
Kurtosis Kurtosis kurtosis	-0.451
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	88850000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.957

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	HYPOXANTHINE GUANINE XANTHINE PHOSPHORIBOSYLTRANSFERASE
Molecular weight formula_weight	26522.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7494

MASKPIEDYGKGKGRIEPMYIPDNTFYNADDFLVPPHCKPYIDKILLPGGLVKDRVEKLAYDIHRTYFGEELHIICILKGSRGFFNLLIDYLATIQKYSGRESSVPPFFEHYVRLKSYQNDNSTGQLTVLSDDLSIFRDKHVLIVEDIVDTGFTLTEFGERLKAVGPKSMRIATLVEKRTDRSNSLKGDFVGFSIEDVWIVGCCYDFNEMFRDFDHVAVLSDAARKKFEKV

来源 Source

来源生物 organism	Toxoplasma gondii
NCBI Class编号 ncbi_taxonomy_id	5811
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	387

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1dbra_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

Domain ID domain_id	d1dbrb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

Domain ID domain_id	d1dbrc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

Domain ID domain_id	d1dbrd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

CATH v4.4 (4 domains)

Domain ID domain_id	1dbrA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	1dbrB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	1dbrC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	1dbrD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

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8. Citations (1)

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Unit-cell length a length_a	65.150 Å
Unit-cell length b length_b	109.220 Å
Unit-cell length c length_c	79.740 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.1680
R_free r_free	—

fit	/app/data/saxs_computation/db/1dbr/1dbr.fit
pddf	/app/data/pr_computation/db/1dbr/1dbr.pr.out
profile	/app/data/saxs_computation/db/1dbr/1dbr.dat

HYPOXANTHINE GUANINE XANTHINE

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

HYPOXANTHINE GUANINE XANTHINE PHOSPHORIBOSYLTRANSFERASE

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