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- PDB-3glx: Crystal Structure Analysis of the DtxR(E175K) complexed with Ni(II) -

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Basic information

Entry
Database: PDB / ID: 3glx
TitleCrystal Structure Analysis of the DtxR(E175K) complexed with Ni(II)
ComponentsDiphtheria toxin repressor
KeywordsTRANSCRIPTION / REPRESSOR / REGULATOR / DTXR / HELIX-TURN-HELIX / METAL ION / ACTIVATION / DNA-BINDING / FERROUS IRON / Cytoplasm / Transcriptional regulation / transcriptional regulator / Iron / Transcription regulation
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 / Ferrous iron transport protein A (FeoA) / 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 / Ferrous iron transport protein A (FeoA) / 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 / SH3 type barrels. / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / PHOSPHATE ION / Diphtheria toxin repressor / Diphtheria toxin repressor
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsD'Aquino, J.A. / Denninger, A. / Moulin, A. / D'Aquino, K.E. / Ringe, D.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Decreased sensitivity to changes in the concentration of metal ions as the basis for the hyperactivity of DtxR(E175K).
Authors: D'Aquino, J.A. / Denninger, A.R. / Moulin, A.G. / D'Aquino, K.E. / Ringe, D.
History
DepositionMar 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_ref_seq_dif ...database_2 / 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 / _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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)25,5323
Polymers25,3781
Non-polymers1542
Water1,15364
1
A: Diphtheria toxin repressor
hetero molecules

A: Diphtheria toxin repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0636
Polymers50,7562
Non-polymers3074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2320 Å2
ΔGint-55 kcal/mol
Surface area22480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.800, 63.800, 108.165
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Diphtheria toxin repressor / Iron-dependent diphtheria tox regulatory element / Tox regulatory factor


Mass: 25377.914 Da / Num. of mol.: 1 / Mutation: E175K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: DIP1414, dtxR / Plasmid: pET-11c-dtxR(E175K) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33120, UniProt: P0DJL7*PLUS
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.95 M Sodium/Potasium Phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.03313 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 9, 2008
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03313 Å / Relative weight: 1
ReflectionRedundancy: 10.4 % / Av σ(I) over netI: 26.63 / Number: 214617 / Rmerge(I) obs: 0.079 / Χ2: 1 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 20646 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.095099.610.0480.99910.2
3.254.0910010.0641.00510.9
2.843.2510010.070.99711
2.582.8410010.0981.00811
2.392.5810010.1220.99311
2.252.3910010.1561.00911
2.142.2510010.2080.99410.9
2.052.1410010.2811.00210.7
1.972.0510010.4190.9879.9
1.91.9792.210.4921.0087
ReflectionResolution: 1.85→50 Å / Num. all: 21162 / Num. obs: 22293 / % possible obs: 99.2 % / Redundancy: 10.4 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.079 / Χ2: 1 / Net I/σ(I): 26.628
Reflection shellResolution: 1.85→1.97 Å / Redundancy: 7 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1880 / Χ2: 1.008 / % possible all: 92.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.21 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.2 Å
Translation2.5 Å49.2 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QQ9

2qq9


Resolution: 1.85→38.65 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.292 / WRfactor Rwork: 0.237 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.966 / SU B: 2.766 / SU ML: 0.087 / SU R Cruickshank DPI: 0.147 / SU Rfree: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.147
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1135 5.1 %RANDOM
Rwork0.221 ---
obs0.224 22265 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.39 Å2 / Biso mean: 34.099 Å2 / Biso min: 12.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.147 Å-
Luzzati sigma a-0.087 Å
Refinement stepCycle: LAST / Resolution: 1.85→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 6 64 1758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221716
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9782335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7925223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.87823.46278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.8315322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6831520
X-RAY DIFFRACTIONr_chiral_restr0.1180.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211253
X-RAY DIFFRACTIONr_mcbond_it1.1021.51073
X-RAY DIFFRACTIONr_mcangle_it1.91221759
X-RAY DIFFRACTIONr_scbond_it3.0353643
X-RAY DIFFRACTIONr_scangle_it4.8274.5568
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 71 -
Rwork0.287 1478 -
all-1549 -
obs--95.56 %

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