SAXSdb — 1c3x

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

PENTOSYLTRANSFERASE

OrganismNot specified

UniProt P81989

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 9–282 Chain B； UniProt 9–282 Chain C； UniProt 9–282	Not recorded	PO4 PHOSPHATE ION × 3 8IG 8-IODO-GUANINE × 3 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.2；298 K；PEG 4000, CACODYLATE, CA-ACETATE, SODIUM PHOSPHATE, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.251

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 1C3X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1QE5 PURINE NUCLEOSIDE PHOSPHORYLASE FROM CELLULOMONAS SP. IN COMPLEX WITH PHOSPHATE Deposited 1999-07-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 9–282（274 aa） Fragment：RESIDUES 9-282 Chain B 9–282（274 aa） Fragment：RESIDUES 9-282 Chain C 9–282（274 aa） Fragment：RESIDUES 9-282	Not recorded	PO4 PHOSPHATE ION × 3 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；PEG 4000, cacodylate, Ca-acetate, sodium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.260

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PUNA_CELSP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–266； UniProt 9–282 Author chain B； PDBConstruct 1–266； UniProt 9–282 Author chain C； PDBConstruct 1–266； UniProt 9–282

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	1c3x
Deposition date deposition_date	1999-07-29
Structure title title	PURINE NUCLEOSIDE PHOSPHORYLASE FROM CELLULOMONAS SP. IN COMPLEX WITH 8-IODO-GUANINE
Keywords keywords	ENZYME, PURINE NUCLEOSIDE PHOSPHORYLASE, TRANSFERASE; 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	29.17 Å
Radius of gyration Rg (electron density) rg_electron	28.22 Å
Forward intensity I(0) i0	119946000.00
Molecular weight molecular_weight	83672.0 kDa
Excluded volume excluded_volume	103560 Å³
Envelope volume envelope_volume	126010 Å³
Hydration-shell volume shell_volume	37052 Å³
Envelope diameter envelope_diameter	91.0 Å
Shell Rg shell_rg	35.92 Å
Envelope Rg envelope_rg	28.25 Å
Shape Rg shape_rg	28.24 Å
Total Rg total_rg	28.88 Å
Total atoms total_atoms	5866
Residues n_residues	798
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	90.3 Å
Rg (real space) rg_real	29.07 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	1.1990e+08
I(0) uncertainty (real space) i0_real_error	1.5980e+06
Rg (reciprocal space) rg_reciprocal	29.12 Å
I(0) (reciprocal space) i0_reciprocal	120000000.0000
Solution quality estimate total_estimate	0.9089
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.1 Å
Skewness Skewness skewness	0.184
Kurtosis Kurtosis kurtosis	-0.581
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	30600000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.944

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	PENTOSYLTRANSFERASE
Molecular weight formula_weight	27546.2 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	6133

PPLDDPATDPFLVARAAADHIAQATGVEGHDMALVLGSGWGGAAELLGEVVAEVPTHEIPGFSSVTRSIRVERADGSVRHALVLGSRTHLYEGKGVRAVVHGVRTAAATGAETLILTNGCGGLNQEWGAGTPVLLSDHINLTARSPLEGPTFVDLTDVYSPRLRELAHRVDPTLPEGVYAQFPGPHYETPAEVRMAGILGADLVGMSTTLEAIAARHCGLEVLGVSLVTNLAAGISPTPLSHAEVIEAGQAAGPRISALLADIAKR

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	8-IODO-GUANINE
Molecular weight formula_weight	277.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	267

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1c3xa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.1 — Purine and uridine phosphorylases

Domain ID domain_id	d1c3xb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.1 — Purine and uridine phosphorylases

Domain ID domain_id	d1c3xc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.2 — Purine and uridine phosphorylases
Family Family family	c.56.2.1 — Purine and uridine phosphorylases

CATH v4.4 (3 domains)

Domain ID domain_id	1c3xA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

Domain ID domain_id	1c3xB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

Domain ID domain_id	1c3xC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1580 — Nucleoside phosphorylase domain

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8. Citations (1)

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Unit-cell length a length_a	63.319 Å
Unit-cell length b length_b	108.340 Å
Unit-cell length c length_c	117.562 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	44.000 Å
R factor r_factor	0.2000
R_work r_work	0.2000
R_free r_free	0.2510

fit	/app/data/saxs_computation/c3/1c3x/1c3x.fit
pddf	/app/data/pr_computation/c3/1c3x/1c3x.pr.out
profile	/app/data/saxs_computation/c3/1c3x/1c3x.dat

PURINE NUCLEOSIDE PHOSPHORYLASE FROM CELLULOMONAS SP. IN COMPLEX WITH 8-IODO-GUANINE

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

PENTOSYLTRANSFERASE

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