1c0w

CRYSTAL STRUCTURE OF THE COBALT-ACTIVATED DIPHTHERIA TOXIN REPRESSOR-DNA COMPLEX REVEALS A METAL BINDING SH-LIKE DOMAIN

Method: X-RAY DIFFRACTION D_max: 115.2 Å Quality: GOOD

▼

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

DIPHTHERIA TOXIN REPRESSOR

Corynebacterium diphtheriae

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 2–226 Chain B； UniProt 2–226 Chain C； UniProt 2–226 Chain D； UniProt 2–226	Not recorded	;DNA (5'-D(PAPTPTPAPGPGPTPTPAPGPCPCPTPAPCPCPCPTPAPAPT)-3') ; × 1 ;DNA (5'-D(PAPTPTPAPGPGPTPTPAPGPGPCPTPAPCPCPCPTPAPAPT)-3') ; × 1 CO COBALT (II) ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 3.20 Å R-free 0.279

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 1C0W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BI0 STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR Deposited 1998-06-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–226（226 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.30 Å R-free 0.296
1BI1 STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR Deposited 1998-06-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–226（226 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.20 Å R-free 0.311
1BI2 STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR Deposited 1998-06-21	Different construct Different mutation/modification 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 1–226（226 aa） Chain B 1–226（226 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.30 Å R-free 0.352
1BI3 STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR Deposited 1998-06-21	Different construct Different mutation/modification 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 1–226（226 aa） Chain B 1–226（226 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.40 Å R-free 0.333
1BYM SOLUTION STRUCTURES OF THE C-TERMINAL DOMAIN OF DIPHTHERIA TOXIN REPRESSOR Deposited 1998-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 130–226（97 aa） Fragment：RESIDUES 130-226	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K	Resolution not provided
1DDN DIPHTHERIA TOX REPRESSOR (C102D MUTANT)/TOX DNA OPERATOR COMPLEX Deposited 1998-06-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–226（226 aa） Chain B 1–226（226 aa） Chain C 1–226（226 aa） Chain D 1–226（226 aa）	Mutation：C102D Mutation：C102D Mutation：C102D Mutation：C102D	NI NICKEL (II) ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.280
1DPR STRUCTURES OF THE APO-AND METAL ION ACTIVATED FORMS OF THE DIPHTHERIA TOX REPRESSOR FROM CORYNEBACTERIUM DIPHTHERIAE Deposited 1995-02-06	Different construct Different mutation/modification 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 1–226（226 aa） Chain B 1–226（226 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.417
1F5T DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL AND DTXR CONSENSUS BINDING SEQUENCE Deposited 2000-06-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–121（121 aa） Chain B 1–121（121 aa） Chain C 1–121（121 aa） Chain D 1–121（121 aa）	Mutation：C102D Mutation：C102D Mutation：C102D Mutation：C102D	NI NICKEL (II) ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100 mM sodium cacodylate pH7.3, 10 mM MgCl2, 2 mM spermine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.00 Å R-free 0.273
1FWZ GLU20ALA DTXR Deposited 2000-09-25	Different construct Different mutation/modification 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 1–226（226 aa）	Mutation：E20A Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；1.6-2.0 ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.285
1G3S CYS102SER DTXR Deposited 2000-10-25	Different construct Different mutation/modification 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 1–226（226 aa）	Mutation：C102S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；Ammonium sulfate, EDTA, glycerol, pH 8.5, VAPOR DIFFUSION, temperature 298K	Resolution 2.40 Å R-free 0.271
1G3T CYS102SER DTXR Deposited 2000-10-25	Different construct Different mutation/modification 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 1–226（226 aa） Chain B 1–226（226 aa）	Mutation：C102S Mutation：C102S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ammonium sulfate, glycerol, EDTA, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.35 Å R-free 0.318
1G3W CD-CYS102SER DTXR Deposited 2000-10-25	Different construct Different mutation/modification 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 1–226（226 aa）	Mutation：C102	CD CADMIUM ION × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ammonium sulfate, glycerol, CdCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.259
1G3Y ARG80ALA DTXR Deposited 2000-10-25	Different construct Different mutation/modification 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 1–226（226 aa）	Mutation：R80A	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；Ammonium sulfate, Zn2+, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.328
1P92 Crystal Structure of (H79A)DtxR Deposited 2003-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–226（226 aa）	Mutation：H79A	BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 400, ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.280
1P92 Crystal Structure of (H79A)DtxR Deposited 2003-05-08	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 A 1–226（226 aa）	Mutation：H79A	BME BETA-MERCAPTOETHANOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 400, ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.280
1QVP C terminal SH3-like domain from Diphtheria toxin Repressor residues 144-226. Deposited 2003-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 144–226（83 aa） Fragment：Residues 144-226	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Pressure ambient NMR sample composition 1-2 mM DtxR144-226 U-15N; 10mM Potassium Phosphate buffer pH6.5 \| 90% H2O/10% D2O NMR sample composition 1-2 mM DtxR144-226 U-15N and U-13C; 10mM Potassium Phosphate buffer pH6.5 \| 90% H2O, 10% D2O; 100% D2O	Resolution not provided
1QW1 Solution Structure of the C-Terminal Domain of DtxR residues 110-226 Deposited 2003-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–226（117 aa） Fragment：RESIDUES 110-226	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Pressure ambient NMR sample composition 1-2 mM DtxR110-226 U-15N, 50 mM Potassium Phosphate, pH 6.5 \| 90% H2O/10% D2O NMR sample composition 1-2 mM DtxR110-226 U-15N U-13C, 50 mM Potassium Phosphate, pH 6.5 \| 100% D2O NMR sample composition 1-2 mM DtxR110-226 U-15N U-13C, 50 mM Potassium Phosphate, pH 6.5 \| 90% H2O/10% D2O	Resolution not provided
1XCV Crystal Structure Of (H79AC102D)Dtxr complexed with Nickel(II) Deposited 2004-09-03	Different construct Different mutation/modification 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 1–139（139 aa）	Mutation：H79A, C102D	NI NICKEL (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；ammonium sulfate, PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.300
2DTR STRUCTURE OF DIPHTHERIA TOXIN REPRESSOR Deposited 1996-07-26	Different construct Different mutation/modification 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 1–226（226 aa）	Not recorded	SO4 SULFATE ION × 2 CO COBALT (II) ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
2QQ9 Crystal Structure of DtxR(D6A C102D) Complexed with Nickel(II) Deposited 2007-07-26	Different construct Different mutation/modification 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 1–226（226 aa）	Mutation：D6A, C102D	NI NICKEL (II) ION × 4 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.2 M Sodium Phosphate, 20% PEG 3350, 5 mM Nickel Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.71 Å R-free 0.291
2QQA Crystal Structure of DtxR(E9A C102D) Complexed with Nickel(II) Deposited 2007-07-26	Different construct Different mutation/modification 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 1–226（226 aa）	Mutation：E9A, C102D	NI NICKEL (II) ION × 4 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.2 M Sodium Phosphate, 20% PEG 3350, 5 mM Nickel Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.256
2QQB Crystal Structure of DtxR(M10A C102D) Complexed with Nickel(II) Deposited 2007-07-26	Different construct Different mutation/modification 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 1–226（226 aa）	Mutation：M10A, C102D	NI NICKEL (II) ION × 4 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.2 M Sodium Phosphate, 20% PEG 3350, 5 mM Nickel Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.92 Å R-free 0.311
2TDX DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL Deposited 1998-06-22	Different construct Different mutation/modification 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 1–226（226 aa）	Mutation：C102D	NI NICKEL (II) ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.321
3GLX Crystal Structure Analysis of the DtxR(E175K) complexed with Ni(II) Deposited 2009-03-12	Different construct Different mutation/modification 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 1–226（226 aa）	Mutation：E175K	NI NICKEL (II) ION × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.95 M Sodium/Potasium Phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.85 Å R-free 0.271

23 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DTXR_CORDI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–225； UniProt 2–226 Author chain B； PDBConstruct 1–225； UniProt 2–226 Author chain C； PDBConstruct 1–225； UniProt 2–226 Author chain D； PDBConstruct 1–225； UniProt 2–226

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1c0w
Deposition date deposition_date	1999-07-22
Structure title title	CRYSTAL STRUCTURE OF THE COBALT-ACTIVATED DIPHTHERIA TOXIN REPRESSOR-DNA COMPLEX REVEALS A METAL BINDING SH-LIKE DOMAIN
Keywords keywords	TOXIN REPRESSOR-DNA COMPLEX, METAL BINDING SH-LIKE DOMAIN, GENE REGULATION-DNA COMPLEX; GENE REGULATION/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	33.59 Å
Radius of gyration Rg (electron density) rg_electron	34.29 Å
Forward intensity I(0) i0	171514000.00
Molecular weight molecular_weight	94769.0 kDa
Excluded volume excluded_volume	114210 Å³
Envelope volume envelope_volume	149540 Å³
Hydration-shell volume shell_volume	37131 Å³
Envelope diameter envelope_diameter	122.9 Å
Shell Rg shell_rg	39.98 Å
Envelope Rg envelope_rg	33.84 Å
Shape Rg shape_rg	34.37 Å
Total Rg total_rg	34.42 Å
Total atoms total_atoms	6575
Residues n_residues	784
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	115.2 Å
Rg (real space) rg_real	33.70 Å
Rg uncertainty (real space) rg_real_error	1.01 Å
I(0) (real space) i0_real	1.7150e+08
I(0) uncertainty (real space) i0_real_error	2.8440e+06
Rg (reciprocal space) rg_reciprocal	33.63 Å
I(0) (reciprocal space) i0_reciprocal	171500000.0000
Solution quality estimate total_estimate	0.8715
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.8 Å
Skewness Skewness skewness	0.437
Kurtosis Kurtosis kurtosis	-0.262
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12720000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.888; Smooth: 0.912

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(PAPTPTPAPGPGPTPTPAPGPCPCPTPAPCPCPCPTPAPAP*T)-3') ;
Molecular weight formula_weight	6397.2 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	6575

ATTAGGTTAGCCTACCCTAAT

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PAPTPTPAPGPGPTPTPAPGPGPCPTPAPCPCPCPTPAPAP*T)-3') ;
Molecular weight formula_weight	6437.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

ATTAGGTTAGGCTACCCTAAT

Entity 3 Entity 3 polymer

Description description	DIPHTHERIA TOXIN REPRESSOR
Molecular weight formula_weight	25218.6 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

KDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAAPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEEL

来源 Source

来源生物 organism	Corynebacterium diphtheriae
NCBI Class编号 ncbi_taxonomy_id	1717
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	8

▼

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1c0wa1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.24 — Iron-dependent repressor protein

Domain ID domain_id	d1c0wa2
Class class	a — All alpha proteins
Fold Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

Domain ID domain_id	d1c0wa3
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
Family Family family	b.34.1.2 — FeoA-like

Domain ID domain_id	d1c0wb1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.24 — Iron-dependent repressor protein

Domain ID domain_id	d1c0wb2
Class class	a — All alpha proteins
Fold Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

Domain ID domain_id	d1c0wb3
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
Family Family family	b.34.1.2 — FeoA-like

Domain ID domain_id	d1c0wc1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.24 — Iron-dependent repressor protein

Domain ID domain_id	d1c0wc2
Class class	a — All alpha proteins
Fold Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

Domain ID domain_id	d1c0wc3
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
Family Family family	b.34.1.2 — FeoA-like

Domain ID domain_id	d1c0wd1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.24 — Iron-dependent repressor protein

Domain ID domain_id	d1c0wd2
Class class	a — All alpha proteins
Fold Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

Domain ID domain_id	d1c0wd3
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
Family Family family	b.34.1.2 — FeoA-like

CATH v4.4 (12 domains)

Domain ID domain_id	1c0wA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1c0wA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

Domain ID domain_id	1c0wA03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1920 —

Domain ID domain_id	1c0wB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1c0wB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

Domain ID domain_id	1c0wB03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

Domain ID domain_id	1c0wC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1c0wC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

Domain ID domain_id	1c0wC03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1920 —

Domain ID domain_id	1c0wD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1c0wD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

Domain ID domain_id	1c0wD03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1920 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	180.200 Å
Unit-cell length b length_b	180.200 Å
Unit-cell length c length_c	151.000 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	32

Space group space_group	P 42 2 2
Space-group number int_tables_number	93
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2490
R_work r_work	0.2490
R_free r_free	0.2790

fit	/app/data/saxs_computation/c0/1c0w/1c0w.fit
pddf	/app/data/pr_computation/c0/1c0w/1c0w.pr.out
profile	/app/data/saxs_computation/c0/1c0w/1c0w.dat

CRYSTAL STRUCTURE OF THE COBALT-ACTIVATED DIPHTHERIA TOXIN REPRESSOR-DNA COMPLEX REVEALS A METAL BINDING SH-LIKE DOMAIN

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

DIPHTHERIA TOXIN 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

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 non-polymer

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)