SAXSdb — 1par

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

PROTEIN (ARC REPRESSOR)

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–DNA Homooligomer Protein × 4 DNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain A； UniProt 1–53 Chain B； UniProt 1–53 Chain C； UniProt 1–53 Chain D； UniProt 1–53	Not recorded	;DNA (5'-D(TPAPTPAPGPTPAPGPAPGPTPGPCPTPTPCPT PAPTPCPAPT)- 3') ; × 1 ;DNA (5'-D(APAPTPGPAPTPAPGPAPAPGPCPAPCPTPCPT PAPCPTPAPT)- 3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；pH 7.40, VAPOR DIFFUSION, HANGING DROP	Resolution 2.60 Å

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 1PAR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ARQ RELAXATION MATRIX REFINEMENT OF THE SOLUTION STRUCTURE OF THE ARC REPRESSOR Deposited 1993-08-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–53（53 aa） Chain B 1–53（53 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1ARR RELAXATION MATRIX REFINEMENT OF THE SOLUTION STRUCTURE OF THE ARC REPRESSOR Deposited 1993-08-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–53（53 aa） Chain B 1–53（53 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1B28 ARC REPRESSOR MYL MUTANT FROM SALMONELLA BACTERIOPHAGE P22 Deposited 1998-12-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–53（53 aa） Chain B 1–53（53 aa）	Mutation：CHAIN A: R31M,E36Y,R40L, CHAIN B: R131M,E136Y,R140L Mutation：CHAIN A: R31M,E36Y,R40L, CHAIN B: R131M,E136Y,R140L	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；303 K；Ionic strength (raw mmCIF value) 50 mM KPI, 150 mM NACL	Resolution not provided
1BAZ ARC REPRESSOR MUTANT PHE10VAL Deposited 1998-04-21	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–53（53 aa） Chain B 1–53（53 aa） Chain C 1–53（53 aa） Chain D 1–53（53 aa）	Mutation：F10V Mutation：F10V Mutation：F10V Mutation：F10V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；PROTEIN WAS CRYSTALLIZED FROM 40-45% SATURATED AMMONIUM PHOSPHATE, PH 8.0, BY MACROSEEDING USING CRYSTALS OF THE WILD TYPE PROTEIN	Resolution 1.90 Å R-free 0.273
1BDT WILD TYPE GENE-REGULATING PROTEIN ARC/DNA COMPLEX Deposited 1998-05-11	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–53（53 aa） Chain B 1–53（53 aa） Chain C 1–53（53 aa） Chain D 1–53（53 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 2.50 Å R-free 0.282
1MYK CRYSTAL STRUCTURE, FOLDING, AND OPERATOR BINDING OF THE HYPERSTABLE ARC REPRESSOR MUTANT PL8 Deposited 1994-10-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–53（53 aa） Chain B 1–53（53 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.277
1MYL SUBSTITUTING HYDROPHOBIC RESIDUES FOR A BURIED SALT BRIDGE ENHANCES PROTEIN STABILITY BUT DOES NOT REDUCE CONFORMATIONAL SPECIFICITY Deposited 1994-10-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–53（53 aa） Chain B 1–53（53 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.293
1MYL SUBSTITUTING HYDROPHOBIC RESIDUES FOR A BURIED SALT BRIDGE ENHANCES PROTEIN STABILITY BUT DOES NOT REDUCE CONFORMATIONAL SPECIFICITY Deposited 1994-10-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–53（53 aa） Chain F 1–53（53 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.293
1MYL SUBSTITUTING HYDROPHOBIC RESIDUES FOR A BURIED SALT BRIDGE ENHANCES PROTEIN STABILITY BUT DOES NOT REDUCE CONFORMATIONAL SPECIFICITY Deposited 1994-10-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–53（53 aa） Chain D 1–53（53 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.293
1NLA Solution Structure of Switch Arc, a Mutant with 3(10) Helices Replacing a Wild-Type Beta-Ribbon Deposited 2003-01-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–53（53 aa） Chain B 1–53（53 aa）	Mutation：N11L, L12N Mutation：N11L, L12N	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.8；303 K；Ionic strength (raw mmCIF value) 20mM phosphate；Pressure ambient NMR measurement conditions pH 4.8；303 K；Ionic strength (raw mmCIF value) 20 mM phosphate；Pressure ambient NMR measurement conditions pH 4.67；303 K；Ionic strength (raw mmCIF value) 20 mM phosphate, 150 mM KCl；Pressure ambient NMR sample composition 4 mM uniform 15N-labelled Arc repressor NL11/LN12 (Switch Arc) \| 90% H2O/10% D2O NMR sample composition 7.5 mM 10% 13C-labelled Arc repressor NL11/LN12 (Switch Arc) \| 90% H2O, 10% D20 NMR sample composition 5 mM uniform 15N-labelled Arc repressor NL11/LN12 (Switch Arc) \| 100% D2O	Resolution not provided
1QTG AVERAGED NMR MODEL OF SWITCH ARC, A DOUBLE MUTANT OF ARC REPRESSOR Deposited 1999-06-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–53（53 aa） Chain B 1–53（53 aa）	Mutation：N11L, L12N Mutation：N11L, L12N	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RARC_BPP22
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–53； UniProt 1–53 Author chain B； PDBConstruct 1–53； UniProt 1–53 Author chain C； PDBConstruct 1–53； UniProt 1–53 Author chain D； PDBConstruct 1–53； UniProt 1–53

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	1par
Deposition date deposition_date	1994-03-22
Structure title title	DNA RECOGNITION BY BETA-SHEETS IN THE ARC REPRESSOR-OPERATOR CRYSTAL STRUCTURE
Keywords keywords	PROTEIN-DNA COMPLEX, DOUBLE HELIX, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
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	22.98 Å
Radius of gyration Rg (electron density) rg_electron	22.05 Å
Forward intensity I(0) i0	37446500.00
Molecular weight molecular_weight	38027.0 kDa
Excluded volume excluded_volume	43698 Å³
Envelope volume envelope_volume	54847 Å³
Hydration-shell volume shell_volume	21430 Å³
Envelope diameter envelope_diameter	77.8 Å
Shell Rg shell_rg	27.97 Å
Envelope Rg envelope_rg	22.07 Å
Shape Rg shape_rg	21.99 Å
Total Rg total_rg	22.80 Å
Total atoms total_atoms	2608
Residues n_residues	252
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	75.2 Å
Rg (real space) rg_real	23.04 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	3.7450e+07
I(0) uncertainty (real space) i0_real_error	4.2740e+05
Rg (reciprocal space) rg_reciprocal	23.02 Å
I(0) (reciprocal space) i0_reciprocal	37450000.0000
Solution quality estimate total_estimate	0.8890
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.3 Å
Skewness Skewness skewness	0.419
Kurtosis Kurtosis kurtosis	-0.354
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4339000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.976

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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	;DNA (5'-D(TPAPTPAPGPTPAPGPAPGPTPGPCPTPTPCPT PAPTPCPAPT)- 3') ;
Molecular weight formula_weight	6756.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E
Atom count atom_count	2653

TATAGTAGAGTGCTTCTATCAT

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APAPTPGPAPTPAPGPAPAPGPCPAPCPTPCPT PAPCPTPAPT)- 3') ;
Molecular weight formula_weight	6743.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

AATGATAGAAGCACTCTACTAT

Entity 3 Entity 3 polymer

Description description	PROTEIN (ARC REPRESSOR)
Molecular weight formula_weight	6238.3 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D

MKGMSKMPQFNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGRIGA

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	45

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1para_
Class class	a — All alpha proteins
Fold Fold fold	a.43 — Ribbon-helix-helix
Superfamily Superfamily superfamily	a.43.1 — Ribbon-helix-helix
Family Family family	a.43.1.1 — Arc/Mnt-like phage repressors

Domain ID domain_id	d1parb_
Class class	a — All alpha proteins
Fold Fold fold	a.43 — Ribbon-helix-helix
Superfamily Superfamily superfamily	a.43.1 — Ribbon-helix-helix
Family Family family	a.43.1.1 — Arc/Mnt-like phage repressors

Domain ID domain_id	d1parc_
Class class	a — All alpha proteins
Fold Fold fold	a.43 — Ribbon-helix-helix
Superfamily Superfamily superfamily	a.43.1 — Ribbon-helix-helix
Family Family family	a.43.1.1 — Arc/Mnt-like phage repressors

Domain ID domain_id	d1pard_
Class class	a — All alpha proteins
Fold Fold fold	a.43 — Ribbon-helix-helix
Superfamily Superfamily superfamily	a.43.1 — Ribbon-helix-helix
Family Family family	a.43.1.1 — Arc/Mnt-like phage repressors

CATH v4.4 (4 domains)

Domain ID domain_id	1parA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily	10 — Met repressor-like

Domain ID domain_id	1parB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily	10 — Met repressor-like

Domain ID domain_id	1parC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily	10 — Met repressor-like

Domain ID domain_id	1parD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily	10 — Met repressor-like

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8. Citations (1)

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Unit-cell length a length_a	65.670 Å
Unit-cell length b length_b	56.730 Å
Unit-cell length c length_c	53.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	21.000 Å
R factor r_factor	0.2250
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/pa/1par/1par.fit
pddf	/app/data/pr_computation/pa/1par/1par.pr.out
profile	/app/data/saxs_computation/pa/1par/1par.dat

DNA RECOGNITION BY BETA-SHEETS IN THE ARC REPRESSOR-OPERATOR CRYSTAL STRUCTURE

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

PROTEIN (ARC REPRESSOR)

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)