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- PDB-2dtr: STRUCTURE OF DIPHTHERIA TOXIN REPRESSOR -

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Basic information

Entry
Database: PDB / ID: 2dtr
TitleSTRUCTURE OF DIPHTHERIA TOXIN REPRESSOR
ComponentsDIPHTHERIA TOXIN REPRESSOR
KeywordsREPRESSOR / TRANSCRIPTION REGULATION / DNA-BINDING / IRON
Function / homology
Function and homology information


transition metal ion binding / SH3 domain binding / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / identical protein binding / cytoplasm
Similarity search - Function
Diphteria toxin repressor, SH3 domain / Diphteria toxin repressor SH3 domain / Iron dependent repressor, metal binding and dimerisation domain / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / : / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain ...Diphteria toxin repressor, SH3 domain / Diphteria toxin repressor SH3 domain / Iron dependent repressor, metal binding and dimerisation domain / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / : / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain / Helix-turn-helix diphteria tox regulatory element / Diphtheria Toxin Repressor; domain 2 / Transcriptional repressor, C-terminal / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Diphtheria toxin repressor / Diphtheria toxin repressor
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsQiu, X. / Pohl, E. / Hol, W.G.
Citation
Journal: Biochemistry / Year: 1996
Title: High-resolution structure of the diphtheria toxin repressor complexed with cobalt and manganese reveals an SH3-like third domain and suggests a possible role of phosphate as co-corepressor.
Authors: Qiu, X. / Pohl, E. / Holmes, R.K. / Hol, W.G.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Purification and Characterization of the Diphtheria Toxin Repressor
Authors: Schmitt, M.P. / Twiddy, E.M. / Holmes, R.K.
History
DepositionJul 26, 1996Processing site: BNL
SupersessionAug 20, 1997ID: 1DTR
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIPHTHERIA TOXIN REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5053
Polymers25,3501
Non-polymers1552
Water2,666148
1
A: DIPHTHERIA TOXIN REPRESSOR
hetero molecules

A: DIPHTHERIA TOXIN REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0106
Polymers50,7002
Non-polymers3104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2510 Å2
ΔGint-85 kcal/mol
Surface area21620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.900, 63.900, 109.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein DIPHTHERIA TOXIN REPRESSOR / DTXR


Mass: 25349.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Strain: C7(-) / Gene: T / Plasmid: PMS298 / Gene (production host): T / Production host: Escherichia coli (E. coli) / References: UniProt: P33120, UniProt: P0DJL7*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 57 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13 mg/mlprotein1drop
20.5 mM1dropCoCl2
350 mMTris-HCl1drop
41.0 Mammonium sulfate1drop
520 mM2-mercaptoethanol1drop
62.0 Mammonium sulfate1reservoir
70.1 MTris-HCl1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 14788 / % possible obs: 78 % / Redundancy: 3 % / Rmerge(I) obs: 0.045
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Num. measured all: 41868 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.25 Å / % possible obs: 52 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
X-PLORphasing
RefinementResolution: 1.9→7 Å / σ(F): 1
Details: 2FO-FC ELECTRON DENSITY IS MISSING FOR RESIDUES 1 - 3, 141 - 147 AND 199 - 200. THESE RESIDUES ARE ASSUMED TO BE DISORDERED. THE EXPERIMENTAL ELECTRON DENSITY IS WEAK OR MISSING FOR RESIDUES 148 - 226.
RfactorNum. reflection
Rwork0.171 -
obs0.171 14336
Refinement stepCycle: LAST / Resolution: 1.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1139 0 6 148 1293
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.0171 / Lowest resolution: 7 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg22.5
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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