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- PDB-6jgx: Crystal structure of the transcriptional regulator CadR from P. p... -

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Basic information

Entry
Database: PDB / ID: 6jgx
TitleCrystal structure of the transcriptional regulator CadR from P. putida in complex with Cadmium(II) and DNA
Components
  • CadR
  • DNA (5'-D(*CP*AP*CP*CP*CP*TP*AP*TP*AP*GP*TP*GP*GP*CP*TP*AP*CP*AP*GP*GP*GP*T)-3')
  • DNA (5'-D(*GP*AP*CP*CP*CP*TP*GP*TP*AP*GP*CP*CP*AP*CP*TP*AP*TP*AP*GP*GP*GP*T)-3')
KeywordsTRANSCRIPTION/DNA / CadR / MerR family / cadmium regulator / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function
Cd(II)/Pb(II)-responsive transcriptional regulator / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / MerR-type HTH domain signature. / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Putative DNA-binding domain superfamily ...Cd(II)/Pb(II)-responsive transcriptional regulator / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / MerR-type HTH domain signature. / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Putative DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA / DNA (> 10) / CadR
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsLiu, X.C. / Gan, J.H. / Chen, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Selective cadmium regulation mediated by a cooperative binding mechanism in CadR.
Authors: Liu, X. / Hu, Q. / Yang, J. / Huang, S. / Wei, T. / Chen, W. / He, Y. / Wang, D. / Liu, Z. / Wang, K. / Gan, J. / Chen, H.
History
DepositionFeb 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CadR
B: CadR
C: DNA (5'-D(*CP*AP*CP*CP*CP*TP*AP*TP*AP*GP*TP*GP*GP*CP*TP*AP*CP*AP*GP*GP*GP*T)-3')
D: DNA (5'-D(*GP*AP*CP*CP*CP*TP*GP*TP*AP*GP*CP*CP*AP*CP*TP*AP*TP*AP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2988
Polymers46,8484
Non-polymers4504
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9910 Å2
ΔGint-94 kcal/mol
Surface area20710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.490, 131.490, 85.118
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 1 - 135 / Label seq-ID: 1 - 135

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein CadR / Cd(II)/Pb(II)-responsive transcriptional regulator


Mass: 16671.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: cadR, BIW19_10095, BL240_26950 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93TP7
#2: DNA chain DNA (5'-D(*CP*AP*CP*CP*CP*TP*AP*TP*AP*GP*TP*GP*GP*CP*TP*AP*CP*AP*GP*GP*GP*T)-3')


Mass: 6752.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas putida (bacteria)
#3: DNA chain DNA (5'-D(*GP*AP*CP*CP*CP*TP*GP*TP*AP*GP*CP*CP*AP*CP*TP*AP*TP*AP*GP*GP*GP*T)-3')


Mass: 6752.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas putida (bacteria)
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd

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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: 4.77 Å3/Da / Density % sol: 74.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: PEG 3350, potassium chloride, magnesium chloride, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 22742 / % possible obs: 98.9 % / Redundancy: 6.2 % / Rsym value: 0.06 / Net I/σ(I): 26.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2213 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JGV

6jgv


Resolution: 2.71→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 11.518 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.244 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23347 1128 5 %RANDOM
Rwork0.20927 ---
obs0.21051 21613 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 85.244 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å2-1.04 Å2-0 Å2
2---2.08 Å20 Å2
3---6.74 Å2
Refinement stepCycle: 1 / Resolution: 2.71→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 896 4 0 3100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0173227
X-RAY DIFFRACTIONr_bond_other_d0.0030.022643
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.74550
X-RAY DIFFRACTIONr_angle_other_deg1.17236084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9245276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.47523.504117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.02615402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.621529
X-RAY DIFFRACTIONr_chiral_restr0.0760.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023069
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02730
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.0428.7621113
X-RAY DIFFRACTIONr_mcbond_other6.038.7591112
X-RAY DIFFRACTIONr_mcangle_it9.48413.1241386
X-RAY DIFFRACTIONr_mcangle_other9.48413.1281387
X-RAY DIFFRACTIONr_scbond_it6.5748.5282114
X-RAY DIFFRACTIONr_scbond_other6.578.5292113
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.20212.7033165
X-RAY DIFFRACTIONr_long_range_B_refined13.66469.1323903
X-RAY DIFFRACTIONr_long_range_B_other13.66269.1293902
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 15860 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.705→2.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 92 -
Rwork0.399 1491 -
obs--96.06 %

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