1f5t

DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL AND DTXR CONSENSUS BINDING SEQUENCE

Method: X-RAY DIFFRACTION D_max: 144.4 Å Quality: GOOD

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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 1–121 Chain B； UniProt 1–121 Chain C； UniProt 1–121 Chain D； UniProt 1–121	Mutation：C102D	43MER DNA CONTAINING DXTR CONSENSUS BINDING SEQUENCE × 1 43MER DNA CONTAINING DXTR CONSENSUS BINDING SEQUENCE × 1 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

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 1F5T	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
1C0W CRYSTAL STRUCTURE OF THE COBALT-ACTIVATED DIPHTHERIA TOXIN REPRESSOR-DNA COMPLEX REVEALS A METAL BINDING SH-LIKE DOMAIN Deposited 1999-07-22	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 2–226（225 aa） Chain B 2–226（225 aa） Chain C 2–226（225 aa） Chain D 2–226（225 aa）	Not recorded	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
1DDN DIPHTHERIA TOX REPRESSOR (C102D MUTANT)/TOX DNA OPERATOR COMPLEX Deposited 1998-06-23	Different construct 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
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 1–121； UniProt 1–121 Author chain B； PDBConstruct 1–121； UniProt 1–121 Author chain C； PDBConstruct 1–121； UniProt 1–121 Author chain D； PDBConstruct 1–121； UniProt 1–121

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	1f5t
Deposition date deposition_date	2000-06-15
Structure title title	DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL AND DTXR CONSENSUS BINDING SEQUENCE
Keywords keywords	;iron-regulated repressor, DNA-protein complex, helix-turn-helix motif, transcription regulator, diphtheria tox repressor, DNA-binding regulatory protein, 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	35.67 Å
Radius of gyration Rg (electron density) rg_electron	34.82 Å
Forward intensity I(0) i0	161908000.00
Molecular weight molecular_weight	82063.0 kDa
Excluded volume excluded_volume	94386 Å³
Envelope volume envelope_volume	135360 Å³
Hydration-shell volume shell_volume	34170 Å³
Envelope diameter envelope_diameter	153.7 Å
Shell Rg shell_rg	38.45 Å
Envelope Rg envelope_rg	35.51 Å
Shape Rg shape_rg	34.77 Å
Total Rg total_rg	35.16 Å
Total atoms total_atoms	5617
Residues n_residues	566
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	144.4 Å
Rg (real space) rg_real	36.02 Å
Rg uncertainty (real space) rg_real_error	1.98 Å
I(0) (real space) i0_real	1.6190e+08
I(0) uncertainty (real space) i0_real_error	3.1000e+06
Rg (reciprocal space) rg_reciprocal	35.80 Å
I(0) (reciprocal space) i0_reciprocal	161900000.0000
Solution quality estimate total_estimate	0.7736
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.4 Å
Skewness Skewness skewness	0.623
Kurtosis Kurtosis kurtosis	0.373
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8231000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.529; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.503; Smooth: 0.963

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	43MER DNA CONTAINING DXTR CONSENSUS BINDING SEQUENCE
Molecular weight formula_weight	13218.5 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	5621

AACATGCAAGGCTAAGGTTAGCCTAACCTTAGCCTTGCATGTT

Entity 2 Entity 2 polymer

Description description	43MER DNA CONTAINING DXTR CONSENSUS BINDING SEQUENCE
Molecular weight formula_weight	13258.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

TTAACATGCAAGGCTAAGGTTAGGCTAACCTTAGCCTTGCATG

Entity 3 Entity 3 polymer

Description description	DIPHTHERIA TOXIN REPRESSOR
Molecular weight formula_weight	13923.0 kDa
Mutation mutation	C102D
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

MKDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEADRWEHVMSDEVERRLVKVLK

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	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1f5ta1
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	d1f5ta2
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	d1f5tb1
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	d1f5tb2
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	d1f5tc1
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	d1f5tc2
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	d1f5td1
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	d1f5td2
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

CATH v4.4 (8 domains)

Domain ID domain_id	1f5tA01
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	1f5tA02
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	1f5tB01
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	1f5tB02
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	1f5tC01
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	1f5tC02
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	1f5tD01
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	1f5tD02
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

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8. Citations (1)

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Unit-cell length a length_a	116.178 Å
Unit-cell length b length_b	116.178 Å
Unit-cell length c length_c	142.919 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 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	48.830 Å
R factor r_factor	0.2450
R_work r_work	0.2450
R_free r_free	0.2730

fit	/app/data/saxs_computation/f5/1f5t/1f5t.fit
pddf	/app/data/pr_computation/f5/1f5t/1f5t.pr.out
profile	/app/data/saxs_computation/f5/1f5t/1f5t.dat

DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL AND DTXR CONSENSUS BINDING SEQUENCE

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 (5)

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

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)