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- PDB-2qq9: Crystal Structure of DtxR(D6A C102D) Complexed with Nickel(II) -

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Basic information

Entry
Database: PDB / ID: 2qq9
TitleCrystal Structure of DtxR(D6A C102D) Complexed with Nickel(II)
ComponentsDiphtheria toxin repressor
Keywordstranscription regulator / REPRESSOR / REGULATOR / DTXR / HELIX-TURN-HELIX / METAL ION / ACTIVATION / DNA-BINDING / FERROUS IRON / Transcription / 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 / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsD'Aquino, J.A. / Lattimer, J.R. / Denninger, A. / D'Aquino, K.E. / Ringe, D.
CitationJournal: Biochemistry / Year: 2007
Title: Role of the N-Terminal Helix in the Metal Ion-Induced Activation of the Diphtheria Toxin Repressor DtxR.
Authors: D'Aquino, J.A. / Lattimer, J.R. / Denninger, A. / D'Aquino, K.E. / Ringe, D.
History
DepositionJul 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 20, 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_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.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.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 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

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Assembly

Deposited unit
A: Diphtheria toxin repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5304
Polymers25,3181
Non-polymers2123
Water2,900161
1
A: Diphtheria toxin repressor
hetero molecules

A: Diphtheria toxin repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0608
Polymers50,6352
Non-polymers4256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area2650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.711, 62.711, 107.414
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-678-

HOH

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Components

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


Mass: 25317.730 Da / Num. of mol.: 1 / Mutation: D6A, C102D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: dtxR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / 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: 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.: 161 / 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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Sodium Phosphate, 20% PEG 3350, 5 mM Nickel Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Apr 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.71→27.16 Å / Num. obs: 21573 / % possible obs: 84 % / Redundancy: 5 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 4.9
Reflection shellResolution: 1.71→1.756 Å / Num. unique all: 919 / % possible all: 48.53

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrysalisProdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P92

1p92


Resolution: 1.71→27.16 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.876 / SU B: 6.58 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.16
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29149 1152 5.1 %RANDOM
Rwork0.23579 ---
obs0.23862 21573 84.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.761 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.161 Å
Refinement stepCycle: LAST / Resolution: 1.71→27.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1683 0 7 161 1851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221764
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.761.9822406
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5145229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.48923.48886
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.08915335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6091522
X-RAY DIFFRACTIONr_chiral_restr0.1370.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021309
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2460.2984
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21213
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2147
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.294
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0481.51125
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53521787
X-RAY DIFFRACTIONr_scbond_it2.6483698
X-RAY DIFFRACTIONr_scangle_it4.0114.5609
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.71→1.756 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.569 39 -
Rwork0.418 919 -
obs--48.53 %
Refinement TLS params.Method: refined / Origin x: -17.8004 Å / Origin y: 28.2732 Å / Origin z: -5.0842 Å
111213212223313233
T-0.1903 Å2-0.0122 Å2-0.0037 Å2--0.188 Å2-0.0062 Å2---0.1591 Å2
L0.005 °20.0123 °20.0618 °2-0.3369 °2-0.0845 °2--0.9468 °2
S0.0069 Å °0.1119 Å °-0.0317 Å °-0.1934 Å °0.0138 Å °0.0566 Å °0.0331 Å °-0.0322 Å °-0.0207 Å °

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