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- PDB-1dpr: STRUCTURES OF THE APO-AND METAL ION ACTIVATED FORMS OF THE DIPHTH... -

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Basic information

Entry
Database: PDB / ID: 1dpr
TitleSTRUCTURES OF THE APO-AND METAL ION ACTIVATED FORMS OF THE DIPHTHERIA TOX REPRESSOR FROM CORYNEBACTERIUM DIPHTHERIAE
ComponentsDIPHTHERIA TOX REPRESSOR
KeywordsTRANSCRIPTION REGULATION / DIPHTHERIA / VIRULENCE / DNA-BINDING / IRON-REGULATION REPRESSOR
Function / homology
Function and homology information


transition metal ion binding / SH3 domain binding / protein dimerization activity / DNA-binding transcription factor activity / 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 FeoA domain / Ferrous iron transporter, core 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 ...Diphteria toxin repressor, SH3 domain / Diphteria toxin repressor SH3 domain / Iron dependent repressor, metal binding and dimerisation domain / Ferrous iron transporter FeoA domain / Ferrous iron transporter, core 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: 3 Å
AuthorsSchiering, N. / Tao, X. / Murphy, J. / Petsko, G.A. / Ringe, D.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Structures of the apo- and the metal ion-activated forms of the diphtheria tox repressor from Corynebacterium diphtheriae.
Authors: Schiering, N. / Tao, X. / Zeng, H. / Murphy, J.R. / Petsko, G.A. / Ringe, D.
#1: Journal: Mol.Microbiol. / Year: 1994
Title: Iron, Dtxr, and the Regulation of Diphtheria Toxin Expression
Authors: Tao, X. / Schiering, N. / Zeng, H. / Ringe, D. / Murphy, J.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Studies of the Diphtheria Tox Repressor from Corynebacterium Diphtheriae
Authors: Schiering, N. / Tao, X. / Murphy, J. / Petsko, G. / Ringe, D.
History
DepositionFeb 6, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Remark 650HELIX HELIX DETERMINATION METHOD: DSSP AND O.
Remark 700SHEET SHEET SHEET_ID: 1; DETERMINATION METHOD: DSSP AND O.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIPHTHERIA TOX REPRESSOR
B: DIPHTHERIA TOX REPRESSOR


Theoretical massNumber of molelcules
Total (without water)50,7002
Polymers50,7002
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-13 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.000, 64.000, 220.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: GLY B 38 - PRO B 39 OMEGA = 144.51 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.507, 0.861, 0.032), (0.86, 0.503, 0.084), (0.057, 0.07, -0.996)
Vector: 0.287, -5.622, 107.468)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 3 .. A 136 B 3 .. B 136 1.491

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Components

#1: Protein DIPHTHERIA TOX REPRESSOR / DTXR


Mass: 25349.795 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Strain: C7(-) / Plasmid: PDR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P33120, UniProt: P0DJL7*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop / Details: Schiering, N., (1994) J.Mol.Biol., 244, 654.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
21.6 Mammonium sulfate1drop
32 %PEG2001drop
41 mMdithiothreitol1drop
5100 mMHEPES1drop
61.6 Mammonium sulfate1reservoir
72 %PEG2001reservoir
81 mMDTT1reservoir
9100 mMHEPES1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 9355 / % possible obs: 83.8 %
Reflection
*PLUS
Highest resolution: 3 Å / Num. measured all: 21855 / Rmerge(I) obs: 0.075

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 3→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.417 -
Rwork0.241 -
obs0.241 7379
Displacement parametersBiso mean: 13.98 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 0 0 2122
Software
*PLUS
Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 7378 / Rfactor obs: 0.233 / Rfactor Rfree: 0.413 / Rfactor Rwork: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.024
X-RAY DIFFRACTIONx_angle_deg4.8

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