SAXSdb — 1bdt

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

PROTEIN (GENE-REGULATING PROTEIN ARC)

Enterobacteria phage P22

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(TPAPTPAPGPTPAPGPAPGPTPGPCPTPTPCPTPAPTPCPAPT)-3') ; × 1 ;DNA (5'-D(APAPTPGPAPTPAPGPAPAPGPCPAPCPTPCPTPAPCPTPAPT)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.5；pH 4.5	Resolution 2.50 Å R-free 0.282

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 1BDT	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
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
1PAR DNA RECOGNITION BY BETA-SHEETS IN THE ARC REPRESSOR-OPERATOR CRYSTAL STRUCTURE Deposited 1994-03-22	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 VAPOR DIFFUSION, HANGING DROP；pH 7.4；pH 7.40, VAPOR DIFFUSION, HANGING DROP	Resolution 2.60 Å
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	1bdt
Deposition date deposition_date	1998-05-11
Structure title title	WILD TYPE GENE-REGULATING PROTEIN ARC/DNA COMPLEX
Keywords keywords	GENE-REGULATING PROTEIN, GENE REGULATION-DNA COMPLEX; GENE REGULATION/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	22.79 Å
Radius of gyration Rg (electron density) rg_electron	21.88 Å
Forward intensity I(0) i0	36984400.00
Molecular weight molecular_weight	37810.0 kDa
Excluded volume excluded_volume	43417 Å³
Envelope volume envelope_volume	53799 Å³
Hydration-shell volume shell_volume	21102 Å³
Envelope diameter envelope_diameter	76.7 Å
Shell Rg shell_rg	27.88 Å
Envelope Rg envelope_rg	21.94 Å
Shape Rg shape_rg	21.82 Å
Total Rg total_rg	22.63 Å
Total atoms total_atoms	2593
Residues n_residues	249
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	75.3 Å
Rg (real space) rg_real	22.85 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	3.6980e+07
I(0) uncertainty (real space) i0_real_error	4.6600e+05
Rg (reciprocal space) rg_reciprocal	22.84 Å
I(0) (reciprocal space) i0_reciprocal	36980000.0000
Solution quality estimate total_estimate	0.8866
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.9 Å
Skewness Skewness skewness	0.414
Kurtosis Kurtosis kurtosis	-0.361
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4110000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.859; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.979

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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(TPAPTPAPGPTPAPGPAPGPTPGPCPTPTPCPTPAPTPCPAPT)-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	2676

TATAGTAGAGTGCTTCTATCAT

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APAPTPGPAPTPAPGPAPAPGPCPAPCPTPCPTPAPCPTPAPT)-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 (GENE-REGULATING PROTEIN ARC)
Molecular weight formula_weight	6238.3 kDa
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

MKGMSKMPQFNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGRIGA

来源 Source

来源生物 organism	Enterobacteria phage P22
NCBI Class编号 ncbi_taxonomy_id	10754
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	83

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1bdta_
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	d1bdtb_
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	d1bdtc_
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	d1bdtd_
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	1bdtA00
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	1bdtB00
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	1bdtC00
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	1bdtD00
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	62.130 Å
Unit-cell length b length_b	56.410 Å
Unit-cell length c length_c	52.330 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.14 °
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	2.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2364
R_work r_work	0.2364
R_free r_free	0.2820

fit	/app/data/saxs_computation/bd/1bdt/1bdt.fit
pddf	/app/data/pr_computation/bd/1bdt/1bdt.pr.out
profile	/app/data/saxs_computation/bd/1bdt/1bdt.dat

WILD TYPE GENE-REGULATING PROTEIN ARC/DNA COMPLEX

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

PROTEIN (GENE-REGULATING PROTEIN ARC)

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

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

来源 Source

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)