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- PDB-1f5t: DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL AND... -

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Basic information

Entry
Database: PDB / ID: 1f5t
TitleDIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL AND DTXR CONSENSUS BINDING SEQUENCE
Components
  • (43MER DNA CONTAINING DXTR CONSENSUS BINDING SEQUENCE) x 2
  • DIPHTHERIA TOXIN REPRESSOR
KeywordsTRANSCRIPTION/DNA / iron-regulated repressor / DNA-protein complex / helix-turn-helix motif / transcription regulator / diphtheria tox repressor / DNA-binding regulatory protein / TRANSCRIPTION-DNA COMPLEX
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
NICKEL (II) ION / DNA / DNA (> 10) / Diphtheria toxin repressor / Diphtheria toxin repressor
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsChen, S. / White, A. / Love, J. / Murphy, J.R. / Ringe, D.
CitationJournal: Biochemistry / Year: 2000
Title: Methyl groups of thymine bases are important for nucleic acid recognition by DtxR.
Authors: Chen, C.S. / White, A. / Love, J. / Murphy, J.R. / Ringe, D.
History
DepositionJun 15, 2000Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 25, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: 43MER DNA CONTAINING DXTR CONSENSUS BINDING SEQUENCE
F: 43MER DNA CONTAINING DXTR CONSENSUS BINDING SEQUENCE
A: DIPHTHERIA TOXIN REPRESSOR
B: DIPHTHERIA TOXIN REPRESSOR
C: DIPHTHERIA TOXIN REPRESSOR
D: DIPHTHERIA TOXIN REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,63914
Polymers82,1696
Non-polymers4708
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.178, 116.178, 142.919
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Cell settingtetragonal
Space group name H-MP41

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Components

#1: DNA chain 43MER DNA CONTAINING DXTR CONSENSUS BINDING SEQUENCE


Mass: 13218.508 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 43MER DNA CONTAINING DXTR CONSENSUS BINDING SEQUENCE


Mass: 13258.532 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein
DIPHTHERIA TOXIN REPRESSOR / IRON-DEPENDENT DIPHTHERIA TOXREGULATORY ELEMENT / TOX REGULATORY FACTOR / TOX REGULON TRANSCRIPTION ...IRON-DEPENDENT DIPHTHERIA TOXREGULATORY ELEMENT / TOX REGULATORY FACTOR / TOX REGULON TRANSCRIPTION REGULATOR DTXR


Mass: 13923.011 Da / Num. of mol.: 4 / Mutation: C102D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P33120, UniProt: P0DJL7*PLUS
#4: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.87 Å3/Da / Density % sol: 79.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM sodium cacodylate pH7.3, 10 mM MgCl2, 2 mM spermine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2MgCl211
3spermine11
4MgCl212
Crystal grow
*PLUS
Details: drop consists of 2 micro litter of protein solution and 1 micro litter of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.5 mMprotein1drop
20.66 mMDNA1drop
327 mMTris-HCl1drop
4320 mM1dropNaCl
50.74 mMdithiothreitol1drop
64.9 mM1dropMgCl2
749 mM1dropKCl
81.48 mM1dropNiCl2
9100 mMsodium cacodylate1reservoir
1010 mM1reservoirMgCl2
112 mMspermine1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92
DetectorType: ADSC QUANTUM / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 37719 / Num. obs: 37719 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 10.5
Reflection
*PLUS
Num. measured all: 520936

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 3→48.83 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 377523.15 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1827 5 %RANDOM
Rwork0.245 ---
obs0.245 36454 95.8 %-
all-36454 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.5 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 54.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.76 Å0.71 Å
Refinement stepCycle: LAST / Resolution: 3→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 1757 8 4 5621
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_improper_angle_d1.09
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.417 294 5.2 %
Rwork0.392 5365 -
obs--89.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PADNA-RNA.TOP
X-RAY DIFFRACTION34AMORE
X-RAY DIFFRACTION44AMORE
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.09

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