SAXSdb — 1b01

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

TRANSCRIPTIONAL REPRESSOR COPG

Streptococcus agalactiae

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 4 PDB declaration: octameric（8） Consistent with all polymer counts	Chain A； UniProt 1–45 Chain B； UniProt 1–45	Fragment：DNA-BINDING PROTEIN	;DNA (5'-D(CPCPCPGPTPGPCPAPCPTPCPAPAPTPGPCPAPAPT)-3') ; × 2 ;DNA (5'-D(GPAPTPTPGPCPAPTPTPGPAPGPTPGPCPAPCPGPG)-3') ; × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.7；MPD, HEPES, pH 6.70, VAPOR DIFFUSION, HANGING DROP	Resolution 2.56 Å R-free 0.316

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 1B01	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EA4 TRANSCRIPTIONAL REPRESSOR COPG/22bp dsDNA COMPLEX Deposited 2000-11-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 20 PDB declaration: 32-meric	Chain A 1–45（45 aa） Fragment：DNA-BINDING PROTEIN Chain B 1–45（45 aa） Fragment：DNA-BINDING PROTEIN Chain D 1–45（45 aa） Fragment：DNA-BINDING PROTEIN Chain E 1–45（45 aa） Fragment：DNA-BINDING PROTEIN Chain F 1–45（45 aa） Fragment：DNA-BINDING PROTEIN Chain G 1–45（45 aa） Fragment：DNA-BINDING PROTEIN Chain H 1–45（45 aa） Fragment：DNA-BINDING PROTEIN Chain J 1–45（45 aa） Fragment：DNA-BINDING PROTEIN Chain K 1–45（45 aa） Fragment：DNA-BINDING PROTEIN Chain L 1–45（45 aa） Fragment：DNA-BINDING PROTEIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；MPD, NACL, NAACO, pH 4.60	Resolution 2.95 Å R-free 0.307
1EA4 TRANSCRIPTIONAL REPRESSOR COPG/22bp dsDNA COMPLEX Deposited 2000-11-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain D 1–45（45 aa） Fragment：DNA-BINDING PROTEIN Chain E 1–45（45 aa） Fragment：DNA-BINDING PROTEIN Chain F 1–45（45 aa） Fragment：DNA-BINDING PROTEIN Chain G 1–45（45 aa） Fragment：DNA-BINDING PROTEIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；MPD, NACL, NAACO, pH 4.60	Resolution 2.95 Å R-free 0.307
1EA4 TRANSCRIPTIONAL REPRESSOR COPG/22bp dsDNA COMPLEX Deposited 2000-11-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain H 1–45（45 aa） Fragment：DNA-BINDING PROTEIN Chain J 1–45（45 aa） Fragment：DNA-BINDING PROTEIN Chain K 1–45（45 aa） Fragment：DNA-BINDING PROTEIN Chain L 1–45（45 aa） Fragment：DNA-BINDING PROTEIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；MPD, NACL, NAACO, pH 4.60	Resolution 2.95 Å R-free 0.307
1EA4 TRANSCRIPTIONAL REPRESSOR COPG/22bp dsDNA COMPLEX Deposited 2000-11-05	Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Homooligomer；Protein × 4 PDB declaration: octameric	Chain A 1–45（45 aa） Fragment：DNA-BINDING PROTEIN Chain B 1–45（45 aa） Fragment：DNA-BINDING PROTEIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；MPD, NACL, NAACO, pH 4.60	Resolution 2.95 Å R-free 0.307
2CPG TRANSCRIPTIONAL REPRESSOR COPG Deposited 1999-11-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–45（45 aa） Fragment：DNA-BINDING PROTEIN Chain B 1–45（45 aa） Fragment：DNA-BINDING PROTEIN	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.7；72% MPD, 0.1 M HEPES PH 6.7, 3% BENZAMIDINE	Resolution 1.60 Å R-free 0.277
2CPG TRANSCRIPTIONAL REPRESSOR COPG Deposited 1999-11-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–45（45 aa） Fragment：DNA-BINDING PROTEIN	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.7；72% MPD, 0.1 M HEPES PH 6.7, 3% BENZAMIDINE	Resolution 1.60 Å R-free 0.277

2 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	COPG_STRAG
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–45； UniProt 1–45 Author chain B； PDBConstruct 1–45； UniProt 1–45

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	1b01
Deposition date deposition_date	1999-11-15
Structure title title	TRANSCRIPTIONAL REPRESSOR COPG/DNA COMPLEX
Keywords keywords	TRANSCRIPTIONAL REPRESSOR, DNA-BINDING PROTEIN, PLASMID, PROTEIN-DNA COMPLEX, GENE REGULATION/DNA, 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	15.92 Å
Radius of gyration Rg (electron density) rg_electron	14.73 Å
Forward intensity I(0) i0	6798420.00
Molecular weight molecular_weight	15431.0 kDa
Excluded volume excluded_volume	17829 Å³
Envelope volume envelope_volume	20991 Å³
Hydration-shell volume shell_volume	12363 Å³
Envelope diameter envelope_diameter	50.1 Å
Shell Rg shell_rg	20.06 Å
Envelope Rg envelope_rg	14.94 Å
Shape Rg shape_rg	14.66 Å
Total Rg total_rg	15.75 Å
Total atoms total_atoms	1052
Residues n_residues	105
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	50.9 Å
Rg (real space) rg_real	15.84 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	6.7980e+06
I(0) uncertainty (real space) i0_real_error	8.1360e+04
Rg (reciprocal space) rg_reciprocal	15.85 Å
I(0) (reciprocal space) i0_reciprocal	6798000.0000
Solution quality estimate total_estimate	0.9012
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.0 Å
Skewness Skewness skewness	0.152
Kurtosis Kurtosis kurtosis	-0.417
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	620300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.999

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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(CPCPCPGPTPGPCPAPCPTPCPAPAPTPGPCPAPAP*T)-3') ;
Molecular weight formula_weight	5749.7 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	1450

CCCGTGCACTCAATGCAAT

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(GPAPTPTPGPCPAPTPTPGPAPGPTPGPCPAPCPGP*G)-3') ;
Molecular weight formula_weight	5900.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

GATTGCATTGAGTGCACGG

Entity 3 Entity 3 polymer

Description description	TRANSCRIPTIONAL REPRESSOR COPG
Molecular weight formula_weight	5124.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQEK

来源 Source

来源生物 organism	Streptococcus agalactiae
NCBI Class编号 ncbi_taxonomy_id	1311
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	13

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1b01a_
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.43.1.3 — CopG-like

Domain ID domain_id	d1b01b_
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.43.1.3 — CopG-like

CATH v4.4 (2 domains)

Domain ID domain_id	1b01A00
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	1b01B00
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 (2)

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Unit-cell length a length_a	40.300 Å
Unit-cell length b length_b	40.300 Å
Unit-cell length c length_c	221.560 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	16

Space group space_group	P 43 2 2
Space-group number int_tables_number	95
Crystal system crystal_system	—

Resolution resolution	2.560 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2470
R_work r_work	0.2470
R_free r_free	0.3160

fit	/app/data/saxs_computation/b0/1b01/1b01.fit
pddf	/app/data/pr_computation/b0/1b01/1b01.pr.out
profile	/app/data/saxs_computation/b0/1b01/1b01.dat

TRANSCRIPTIONAL REPRESSOR COPG/DNA COMPLEX

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

TRANSCRIPTIONAL REPRESSOR COPG

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)