SAXSdb — 1a97

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

XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE

Escherichia coli

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 3–150 Chain B； UniProt 3–150 Chain C； UniProt 3–150 Chain D； UniProt 3–150	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

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 1A97	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
1A98 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 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
1NUL XPRTASE FROM E. COLI Deposited 1996-10-15	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）	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

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 1–148； UniProt 3–150 Author chain B； PDBConstruct 1–148； UniProt 3–150 Author chain C； PDBConstruct 1–148； UniProt 3–150 Author chain D； PDBConstruct 1–148； UniProt 3–150

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	1a97
Deposition date deposition_date	1998-04-16
Structure title title	XPRTASE FROM E. COLI COMPLEXED WITH GMP
Keywords keywords	PHOSPHORIBOSYLTRANSFERASE, TRANSFERASE, PURINE SALVAGE ENZYME, GLYCOSYLTRANSFERASE; 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	27.23 Å
Radius of gyration Rg (electron density) rg_electron	25.86 Å
Forward intensity I(0) i0	62285500.00
Molecular weight molecular_weight	61890.0 kDa
Excluded volume excluded_volume	77567 Å³
Envelope volume envelope_volume	94807 Å³
Hydration-shell volume shell_volume	30422 Å³
Envelope diameter envelope_diameter	85.9 Å
Shell Rg shell_rg	33.26 Å
Envelope Rg envelope_rg	26.02 Å
Shape Rg shape_rg	25.88 Å
Total Rg total_rg	26.59 Å
Total atoms total_atoms	4373
Residues n_residues	581
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	83.1 Å
Rg (real space) rg_real	27.19 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	6.2290e+07
I(0) uncertainty (real space) i0_real_error	8.2840e+05
Rg (reciprocal space) rg_reciprocal	27.21 Å
I(0) (reciprocal space) i0_reciprocal	62290000.0000
Solution quality estimate total_estimate	0.9048
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.7 Å
Skewness Skewness skewness	0.292
Kurtosis Kurtosis kurtosis	-0.554
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16330000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.915

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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	16527.0 kDa
EC 编号 ec_number	2.4.2.22
Mutation mutation	C59A
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	4421

EKYIVTWDMLQIHARKLASRLMPSEQWKGIIAVSRGGLVPGALLARELGIRHVDTVAISSYDHDNQRELKVLKRAEGDGEGFIVIDDLVDTGGTAVAIREMYPKAHFVTIFAKPAGRPLVDDYVVDIPQDTWIEQPWDMGVVFVPPIS

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	BORIC ACID
Molecular weight formula_weight	61.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	GUANOSINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	363.2 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	48

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1a97a_
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	d1a97b_
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	d1a97c_
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	d1a97d_
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	1a97A00
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	1a97B00
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	1a97C00
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	1a97D00
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	94.042 Å
Unit-cell length b length_b	94.042 Å
Unit-cell length c length_c	166.914 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	32

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2330
R_work r_work	0.2330
R_free r_free	0.2630

fit	/app/data/saxs_computation/a9/1a97/1a97.fit
pddf	/app/data/pr_computation/a9/1a97/1a97.pr.out
profile	/app/data/saxs_computation/a9/1a97/1a97.dat

XPRTASE FROM E. COLI COMPLEXED WITH GMP

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