SAXSdb — 1nul

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

XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–152 Chain B； UniProt 1–152	Not recorded	SO4 SULFATE ION × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；XPRT WAS CRYSTALLISED FROM 18 - 23% PEG 4000, 0.1 M LI2SO4 IN 0.1 M TRIS-HCL, PH 8., pH 8.0	Resolution 1.80 Å R-free 0.234

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 1NUL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A95 XPRTASE FROM E. COLI COMPLEXED WITH MG:CPRPP AND GUANINE Deposited 1998-04-16	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 1–152（152 aa） Chain B 1–152（152 aa） Chain C 1–152（152 aa） Chain D 1–152（152 aa）	Not recorded	BO3 BORIC ACID × 2 MG MAGNESIUM ION × 2 PCP 1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE × 2 GUN GUANINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；XPRT WAS CRYSTALLISED FROM 15-20% PEG4000, 0.1 M BORATE PH 9.0, 0.1 M AMMONIUM PHOSPHATE	Resolution 2.00 Å R-free 0.232
1A96 XPRTASE FROM E. COLI WITH BOUND CPRPP AND XANTHINE Deposited 1998-04-16	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 1–152（152 aa） Chain B 1–152（152 aa） Chain C 1–152（152 aa） Chain D 1–152（152 aa）	Not recorded	BO3 BORIC ACID × 2 MG MAGNESIUM ION × 2 PCP 1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE × 2 XAN XANTHINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；XPRT WAS CRYSTALLISED FROM 15 - 20% PEG 4000, 0.1 M AMMONIUM SULPHATE IN 0.1 M BORATE, PH 9., pH 9.0	Resolution 2.00 Å R-free 0.244
1A97 XPRTASE FROM E. COLI COMPLEXED WITH GMP Deposited 1998-04-16	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 3–150（148 aa） Chain B 3–150（148 aa） Chain C 3–150（148 aa） Chain D 3–150（148 aa）	Mutation：C59A Mutation：C59A Mutation：C59A Mutation：C59A	BO3 BORIC ACID × 4 5GP GUANOSINE-5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；XPRT WAS CRYSTALLISED FROM 15 - 20% PEG 4000, 0.1 M AMMONIUM PHOSPHATE IN 0.1 M BORATE, PH 9., pH 9.0	Resolution 2.60 Å R-free 0.263
1A98 XPRTASE FROM E. COLI COMPLEXED WITH GMP Deposited 1998-04-16	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 1–152（152 aa） Chain B 1–152（152 aa）	Mutation：C59A Mutation：C59A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；XPRT WAS CRYSTALLIZED FROM 20% PEG4000 IN 0.1 M TRIS-HCL, pH 8.0	Resolution 2.25 Å R-free 0.224

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

View Construct and Data Evidence

UniProt name	XGPT_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–152； UniProt 1–152 Author chain B； PDBConstruct 1–152； UniProt 1–152

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	1nul
Deposition date deposition_date	1996-10-15
Structure title title	XPRTASE FROM E. COLI
Keywords keywords	PHOSPHORIBOSYLTRANSFERASE, TRANSFERASE, PURINE SALVAGE ENZYME; PHOSPHORIBOSYLTRANSFERASE
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	20.43 Å
Radius of gyration Rg (electron density) rg_electron	19.37 Å
Forward intensity I(0) i0	15290500.00
Molecular weight molecular_weight	30396.0 kDa
Excluded volume excluded_volume	38484 Å³
Envelope volume envelope_volume	46611 Å³
Hydration-shell volume shell_volume	20153 Å³
Envelope diameter envelope_diameter	74.3 Å
Shell Rg shell_rg	25.93 Å
Envelope Rg envelope_rg	20.49 Å
Shape Rg shape_rg	19.38 Å
Total Rg total_rg	20.33 Å
Total atoms total_atoms	2139
Residues n_residues	278
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	70.4 Å
Rg (real space) rg_real	20.43 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	1.5290e+07
I(0) uncertainty (real space) i0_real_error	2.1960e+05
Rg (reciprocal space) rg_reciprocal	20.43 Å
I(0) (reciprocal space) i0_reciprocal	15290000.0000
Solution quality estimate total_estimate	0.5886
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.1 Å
Skewness Skewness skewness	0.443
Kurtosis Kurtosis kurtosis	0.091
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3743000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.694; Stabil: 0.997; Sysdev: 0.193; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
Molecular weight formula_weight	16991.6 kDa
EC 编号 ec_number	2.4.2.22
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2377

MSEKYIVTWDMLQIHARKLASRLMPSEQWKGIIAVSRGGLVPGALLARELGIRHVDTVCISSYDHDNQRELKVLKRAEGDGEGFIVIDDLVDTGGTAVAIREMYPKAHFVTIFAKPAGRPLVDDYVVDIPQDTWIEQPWDMGVVFVPPISGR

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	212

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1nula_
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	d1nulb_
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 (2 domains)

Domain ID domain_id	1nulA00
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	1nulB00
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 (2)

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Unit-cell length a length_a	59.200 Å
Unit-cell length b length_b	92.700 Å
Unit-cell length c length_c	53.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1920
R_work r_work	0.1920
R_free r_free	0.2340

fit	/app/data/saxs_computation/nu/1nul/1nul.fit
pddf	/app/data/pr_computation/nu/1nul/1nul.pr.out
profile	/app/data/saxs_computation/nu/1nul/1nul.dat

XPRTASE FROM E. COLI

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

XANTHINE-GUANINE 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

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