1ea4

TRANSCRIPTIONAL REPRESSOR COPG/22bp dsDNA COMPLEX

Method: X-RAY DIFFRACTION D_max: 137.9 Å Quality: REASONABLE

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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 × 20 DNA 12 PDB declaration: 32-meric（32） Consistent with all polymer counts	Chain A； UniProt 1–45 Chain B； UniProt 1–45 Chain D； UniProt 1–45 Chain E； UniProt 1–45 Chain F； UniProt 1–45 Chain G； UniProt 1–45 Chain H； UniProt 1–45 Chain J； UniProt 1–45 Chain K； UniProt 1–45 Chain L； UniProt 1–45	Fragment：DNA-BINDING PROTEIN	;DNA (5'-D(TPAPAPCPCPGPTPGP CPAPCPTPCPAPAPTPGPCPAPAPTPC)-3') ; × 6 ;DNA(5'-D(APGPAPTPTPGPCPAPTP TPGPAPGPTPGPCPAPCPGPGPTPT)-3') ; × 6	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.6；MPD, NACL, NAACO, pH 4.60	Resolution 2.95 Å R-free 0.307
2	Protein–DNA Homooligomer Protein × 4 DNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain D； UniProt 1–45 Chain E； UniProt 1–45 Chain F； UniProt 1–45 Chain G； UniProt 1–45	Fragment：DNA-BINDING PROTEIN	;DNA (5'-D(TPAPAPCPCPGPTPGP CPAPCPTPCPAPAPTPGPCPAPAPTPC)-3') ; × 1 ;DNA(5'-D(APGPAPTPTPGPCPAPTP TPGPAPGPTPGPCPAPCPGPGPTPT)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.6；MPD, NACL, NAACO, pH 4.60	Resolution 2.95 Å R-free 0.307
3	Protein–DNA Homooligomer Protein × 4 DNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain H； UniProt 1–45 Chain J； UniProt 1–45 Chain K； UniProt 1–45 Chain L； UniProt 1–45	Fragment：DNA-BINDING PROTEIN	;DNA (5'-D(TPAPAPCPCPGPTPGP CPAPCPTPCPAPAPTPGPCPAPAPTPC)-3') ; × 1 ;DNA(5'-D(APGPAPTPTPGPCPAPTP TPGPAPGPTPGPCPAPCPGPGPTPT)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.6；MPD, NACL, NAACO, pH 4.60	Resolution 2.95 Å R-free 0.307
4	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(TPAPAPCPCPGPTPGP CPAPCPTPCPAPAPTPGPCPAPAPTPC)-3') ; × 2 ;DNA(5'-D(APGPAPTPTPGPCPAPTP TPGPAPGPTPGPCPAPCPGPGPTPT)-3') ; × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.6；MPD, NACL, NAACO, pH 4.60	Resolution 2.95 Å R-free 0.307

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 1EA4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B01 TRANSCRIPTIONAL REPRESSOR COPG/DNA COMPLEX Deposited 1999-11-15	Different experimental conditions Different structure-quality metrics	Assembly 1 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 VAPOR DIFFUSION, HANGING DROP；pH 6.7；MPD, HEPES, pH 6.70, VAPOR DIFFUSION, HANGING DROP	Resolution 2.56 Å R-free 0.316
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 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	REPA_STRPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–45； UniProt 1–45 Author chain B； PDBConstruct 1–45； UniProt 1–45 Author chain D； PDBConstruct 1–45； UniProt 1–45 Author chain E； PDBConstruct 1–45； UniProt 1–45 Author chain F； PDBConstruct 1–45； UniProt 1–45 Author chain G； PDBConstruct 1–45； UniProt 1–45 Author chain H； PDBConstruct 1–45； UniProt 1–45 Author chain J； PDBConstruct 1–45； UniProt 1–45 Author chain K； PDBConstruct 1–45； UniProt 1–45 Author chain L； 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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ea4
Deposition date deposition_date	2000-11-05
Structure title title	TRANSCRIPTIONAL REPRESSOR COPG/22bp dsDNA 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	39.39 Å
Radius of gyration Rg (electron density) rg_electron	39.29 Å
Forward intensity I(0) i0	156613000.00
Molecular weight molecular_weight	80552.0 kDa
Excluded volume excluded_volume	92341 Å³
Envelope volume envelope_volume	134110 Å³
Hydration-shell volume shell_volume	32217 Å³
Envelope diameter envelope_diameter	144.1 Å
Shell Rg shell_rg	39.15 Å
Envelope Rg envelope_rg	38.90 Å
Shape Rg shape_rg	39.24 Å
Total Rg total_rg	39.38 Å
Total atoms total_atoms	5482
Residues n_residues	538
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	137.9 Å
Rg (real space) rg_real	40.13 Å
Rg uncertainty (real space) rg_real_error	1.53 Å
I(0) (real space) i0_real	1.5660e+08
I(0) uncertainty (real space) i0_real_error	3.0570e+06
Rg (reciprocal space) rg_reciprocal	39.68 Å
I(0) (reciprocal space) i0_reciprocal	156500000.0000
Solution quality estimate total_estimate	0.7413
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	27.6 Å
Skewness Skewness skewness	0.561
Kurtosis Kurtosis kurtosis	-0.478
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9600000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.574; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.355; Smooth: 0.557

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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	TRANSCRIPTIONAL REPRESSOR COPG
Molecular weight formula_weight	5124.1 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E,F,G,H,J,K,L
Atom count atom_count	6013

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 2 Entity 2 polymer

Description description	;DNA (5'-D(TPAPAPCPCPGPTPGP CPAPCPTPCPAPAPTPGPCPAPAPTPC)-3') ;
Molecular weight formula_weight	6680.3 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	U,W,Y

TAACCGTGCACTCAATGCAATC

Entity 3 Entity 3 polymer

Description description	;DNA(5'-D(APGPAPTPTPGPCPAPTP TPGPAPGPTPGPCPAPCPGPGPTPT)-3') ;
Molecular weight formula_weight	6822.4 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	V,X,Z

AGATTGCATTGAGTGCACGGTT

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	101

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7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1ea4a_
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	d1ea4b_
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	d1ea4d_
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	d1ea4e_
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	d1ea4f_
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	d1ea4g_
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	d1ea4h_
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	d1ea4j_
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	d1ea4k_
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	d1ea4l_
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 (10 domains)

Domain ID domain_id	1ea4A00
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	1ea4B00
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	1ea4D00
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	1ea4E00
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	1ea4F00
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	1ea4G00
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	1ea4H00
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	1ea4J00
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	1ea4K00
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	1ea4L00
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 (3)

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Unit-cell length a length_a	213.400 Å
Unit-cell length b length_b	76.040 Å
Unit-cell length c length_c	50.520 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	40

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2300
R_work r_work	0.2300
R_free r_free	0.3070

fit	/app/data/saxs_computation/ea/1ea4/1ea4.fit
pddf	/app/data/pr_computation/ea/1ea4/1ea4.pr.out
profile	/app/data/saxs_computation/ea/1ea4/1ea4.dat

TRANSCRIPTIONAL REPRESSOR COPG/22bp dsDNA 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

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)