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

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Basic information

Entry
Database: PDB / ID: 6jgw
TitleCrystal structure of the transcriptional regulator CadR from P. putida in complex with DNA
Components
  • (DNA (27-MER)) x 2
  • CadR
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 / MerR-type HTH domain signature. / : / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / MerR-type HTH domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / CadR
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: CadR
A: CadR
C: DNA (27-MER)
D: DNA (27-MER)


Theoretical massNumber of molelcules
Total (without water)49,9364
Polymers49,9364
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-54 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.967, 54.541, 86.259
Angle α, β, γ (deg.)90.00, 100.37, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 116 / Label seq-ID: 1 - 116

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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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 (27-MER)


Mass: 8338.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas putida (bacteria)
#3: DNA chain DNA (27-MER)


Mass: 8254.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas putida (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.15 Å3/Da / Density % sol: 60.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: MPEG 2000, potassium thiocyanate

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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: Nov 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 15413 / % possible obs: 99.5 % / Redundancy: 5.8 % / Rsym value: 0.1 / Net I/σ(I): 15.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1527 / % possible all: 99.6

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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: 2.8→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 15.016 / SU ML: 0.278 / Cross valid method: THROUGHOUT / ESU R: 0.648 / ESU R Free: 0.331 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2539 773 5 %RANDOM
Rwork0.20407 ---
obs0.20654 14632 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 67.28 Å2
Baniso -1Baniso -2Baniso -3
1--3.01 Å2-0 Å2-0.95 Å2
2---7.25 Å2-0 Å2
3---9.94 Å2
Refinement stepCycle: 1 / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 1101 0 3 3041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0163189
X-RAY DIFFRACTIONr_bond_other_d0.0030.022514
X-RAY DIFFRACTIONr_angle_refined_deg1.361.6424535
X-RAY DIFFRACTIONr_angle_other_deg1.31635796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.865237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.45623.333108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.77615365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9471528
X-RAY DIFFRACTIONr_chiral_restr0.0780.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022864
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02719
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_it4.0776.1960
X-RAY DIFFRACTIONr_mcbond_other4.0646.098959
X-RAY DIFFRACTIONr_mcangle_it6.2889.1231193
X-RAY DIFFRACTIONr_mcangle_other6.2919.1271194
X-RAY DIFFRACTIONr_scbond_it6.2187.2532229
X-RAY DIFFRACTIONr_scbond_other6.2177.2522230
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.96710.7933343
X-RAY DIFFRACTIONr_long_range_B_refined13.29657.2244001
X-RAY DIFFRACTIONr_long_range_B_other13.29557.2274002
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 13710 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.801→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 56 -
Rwork0.336 995 -
obs--92.44 %

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