SAXSdb — 1a4x

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

PYRIMIDINE OPERON REGULATORY 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 1–181 Chain B； UniProt 1–181	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

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 1A4X	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 mutation/modification 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
4P82 Structure of PyrR protein from Bacillus subtilis Deposited 2014-03-30	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–179（178 aa）	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

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 1–181； UniProt 1–181 Author chain B； PDBConstruct 1–181； UniProt 1–181

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	1a4x
Deposition date deposition_date	1998-02-08
Structure title title	PYRR, THE BACILLUS SUBTILIS PYRIMIDINE BIOSYNTHETIC OPERON REPRESSOR, HEXAMERIC FORM
Keywords keywords	;TRANSCRIPTION REGULATION, ATTENUATION PROTEIN, RNA-BINDING PROTEIN, PYRIMIDINE BIOSYNTHESIS, TRANSFERASE, PRTASE, PHOSPHORIBOSYLTRANSFERASE, BIFUNCTIONAL ENZYME ;; TRANSCRIPTION REGULATION
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	22.11 Å
Radius of gyration Rg (electron density) rg_electron	21.02 Å
Forward intensity I(0) i0	24180500.00
Molecular weight molecular_weight	37286.0 kDa
Excluded volume excluded_volume	46734 Å³
Envelope volume envelope_volume	55322 Å³
Hydration-shell volume shell_volume	22024 Å³
Envelope diameter envelope_diameter	74.6 Å
Shell Rg shell_rg	27.49 Å
Envelope Rg envelope_rg	21.16 Å
Shape Rg shape_rg	21.05 Å
Total Rg total_rg	21.76 Å
Total atoms total_atoms	2611
Residues n_residues	334
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	70.7 Å
Rg (real space) rg_real	22.06 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	2.4180e+07
I(0) uncertainty (real space) i0_real_error	3.3510e+05
Rg (reciprocal space) rg_reciprocal	22.07 Å
I(0) (reciprocal space) i0_reciprocal	24180000.0000
Solution quality estimate total_estimate	0.8180
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	25.3 Å
Skewness Skewness skewness	0.287
Kurtosis Kurtosis kurtosis	-0.422
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5834000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 0.999; Sysdev: 1.000; 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 (3)

Entity 1 Entity 1 polymer

Description description	PYRIMIDINE OPERON REGULATORY PROTEIN PYRR
Molecular weight formula_weight	20290.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2908

MNQKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGNPVTVGEIDITLYRDDLSKKTSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYENE

来源 Source

来源生物 organism	Bacillus subtilis
NCBI Class编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	237

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1a4xa_
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	d1a4xb_
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	1a4xA00
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	1a4xB00
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	100.580 Å
Unit-cell length b length_b	100.580 Å
Unit-cell length c length_c	275.150 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2110
R_work r_work	0.2110
R_free r_free	0.2470

fit	/app/data/saxs_computation/a4/1a4x/1a4x.fit
pddf	/app/data/pr_computation/a4/1a4x/1a4x.pr.out
profile	/app/data/saxs_computation/a4/1a4x/1a4x.dat

PYRR, THE BACILLUS SUBTILIS PYRIMIDINE BIOSYNTHETIC OPERON REPRESSOR, HEXAMERIC FORM

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

PYRIMIDINE OPERON REGULATORY 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