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- PDB-2tdx: DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL -

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Basic information

Entry
Database: PDB / ID: 2tdx
TitleDIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL
ComponentsDIPHTHERIA TOX REPRESSOR
KeywordsDNA BINDING PROTEIN / DNA-BINDING REGULATORY PROTEIN / DIPHTHERIA TOX REPRESSOR / TRANSCRIPTION REGULATION / DNA-BINDING PROTEIN / IRON-REGULATED REPRESSOR
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
NICKEL (II) ION / Diphtheria toxin repressor / Diphtheria toxin repressor
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.4 Å
AuthorsWhite, A. / Ding, X. / Zheng, H. / Schiering, N. / Ringe, D. / Murphy, J.R.
Citation
Journal: Nature / Year: 1998
Title: Structure of the metal-ion-activated diphtheria toxin repressor/tox operator complex.
Authors: White, A. / Ding, X. / vanderSpek, J.C. / Murphy, J.R. / Ringe, D.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: Identification of the Primary Metal Ion-Activation Sites of the Diphtheria Tox Repressor by X-Ray Crystallography and Site-Directed Mutational Analysis
Authors: Ding, X. / Zeng, H. / Schiering, N. / Ringe, D. / Murphy, J.R.
#2: Journal: Structure / Year: 1995
Title: Three-Dimensional Structure of the Diphtheria Toxin Repressor in Complex with Divalent Cation Co-Repressors
Authors: Qiu, X. / Verlinde, C.L. / Zhang, S. / Schmitt, M.P. / Holmes, R.K. / Hol, W.G.
#3: 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.
History
DepositionJun 22, 1998Processing site: BNL
SupersessionOct 14, 1998ID: 1TDX
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_keywords / struct_ref_seq_dif / struct_sheet / 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_keywords.text / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 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
A: DIPHTHERIA TOX REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4793
Polymers25,3621
Non-polymers1172
Water46826
1
A: DIPHTHERIA TOX REPRESSOR
hetero molecules

A: DIPHTHERIA TOX REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9586
Polymers50,7232
Non-polymers2354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2420 Å2
ΔGint-62 kcal/mol
Surface area13450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.500, 64.500, 105.700
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 TOX REPRESSOR / DTXR


Mass: 25361.740 Da / Num. of mol.: 1 / Mutation: C102D
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH NICKEL (NI) / Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: DTXR / Plasmid: PET11C / Production host: Escherichia coli (E. coli) / References: UniProt: P33120, UniProt: P0DJL7*PLUS
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 4.03 Å3/Da / Density % sol: 70 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein-DNA mixture1drop
2100 mMTris1drop
36-12 %PEG40001reservoir
410 mM1reservoirMgCl2
5100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.32→55 Å / Num. obs: 9464 / % possible obs: 80.6 % / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Rmerge(I) obs: 0.041

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
R-AXISdata reduction
R-AXISdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: APO-DTXR (PDB ENTRY 1DPR)

1dpr


Resolution: 2.4→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.321 897 10 %RANDOM
Rwork0.246 ---
obs0.246 8425 84 %-
Displacement parametersBiso mean: 27 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1101 0 2 26 1129
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_deg1.33
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.69
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
LS refinement shellResolution: 2.4→2.58 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.34 146 7.3 %
Rwork0.3 1197 -
obs--67.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPH19.PEP
X-RAY DIFFRACTION2PARAM_NI_AW.PARTOP_NI_AW.PAR
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.69
LS refinement shell
*PLUS
Rfactor Rwork: 0.3

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