SAXSdb — 4p82

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

Bifunctional protein PyrR

Bacillus subtilis

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 2–179	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；2.5 M NaCl, 0.1M Acetate pH 4.5, 0.2M Li2SO4	Resolution 1.30 Å R-free 0.206

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 4P82	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A3C PYRR, THE BACILLUS SUBTILIS PYRIMIDINE BIOSYNTHETIC OPERON REPRESSOR, DIMERIC FORM Deposited 1998-01-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–181（181 aa）	Not recorded	SM SAMARIUM (III) ION × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.1；PROTEIN WAS CRYSTALLIZED FROM 13-16% PEG 6000, 300 MM AMMONIUM SULFATE, 0.2% BETA-OCTYLGLUCOSIDE, 50 MM SODIUM SUCCINATE, PH 5.1, AND 1 MM SAMARIUM NITRATE.	Resolution 1.60 Å R-free 0.233
1A4X PYRR, THE BACILLUS SUBTILIS PYRIMIDINE BIOSYNTHETIC OPERON REPRESSOR, HEXAMERIC FORM Deposited 1998-02-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–181（181 aa） Chain B 1–181（181 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.1；PROTEIN WAS CRYSTALLIZED FROM 14-16% PEG 6000, 300 MM AMMONIUM SULFATE, 0.2% BETA-OCTYLGLUCOSIDE, 50 MM SODIUM SUCCINATE, PH 5.1. HEXAGONAL SETTING FOR R 3 2.	Resolution 2.30 Å R-free 0.247

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

View Construct and Data Evidence

UniProt name	PYRR_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–180； UniProt 2–179

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	4p82
Deposition date deposition_date	2014-03-30
Structure title title	Structure of PyrR protein from Bacillus subtilis
Keywords keywords	RNA binding proteins, reconstructed amino acid sequence, UNKNOWN FUNCTION; UNKNOWN FUNCTION
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	17.70 Å
Radius of gyration Rg (electron density) rg_electron	16.31 Å
Forward intensity I(0) i0	7859030.00
Molecular weight molecular_weight	20121.0 kDa
Excluded volume excluded_volume	25143 Å³
Envelope volume envelope_volume	29381 Å³
Hydration-shell volume shell_volume	15264 Å³
Envelope diameter envelope_diameter	58.8 Å
Shell Rg shell_rg	22.24 Å
Envelope Rg envelope_rg	16.71 Å
Shape Rg shape_rg	16.32 Å
Total Rg total_rg	17.31 Å
Total atoms total_atoms	1409
Residues n_residues	180
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	60.0 Å
Rg (real space) rg_real	17.62 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	7.8590e+06
I(0) uncertainty (real space) i0_real_error	8.6620e+04
Rg (reciprocal space) rg_reciprocal	17.63 Å
I(0) (reciprocal space) i0_reciprocal	7859000.0000
Solution quality estimate total_estimate	0.8676
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.4 Å
Skewness Skewness skewness	0.240
Kurtosis Kurtosis kurtosis	-0.244
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1359000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.771; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.968

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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	Bifunctional protein PyrR
Molecular weight formula_weight	20432.4 kDa
EC 编号 ec_number	2.4.2.9
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1649

GSNQKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGNPVTVGEIDITLYRDDLSKKTSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYENEK

来源 Source

来源生物 organism	Bacillus subtilis
NCBI Class编号 ncbi_taxonomy_id	224308
宿主生物 host_organism	Escherichia coli BL21(DE3)

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	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	153

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4p82a1
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	d4p82a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4p82a3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	4p82A00
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	76.540 Å
Unit-cell length b length_b	57.600 Å
Unit-cell length c length_c	54.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	128.39 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	42.930 Å
R factor r_factor	0.1801
R_work r_work	0.1788
R_free r_free	0.2057

fit	/app/data/saxs_computation/p8/4p82/4p82.fit
pddf	/app/data/pr_computation/p8/4p82/4p82.pr.out
profile	/app/data/saxs_computation/p8/4p82/4p82.dat

Structure of PyrR protein from Bacillus subtilis

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

Bifunctional protein PyrR

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