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- PDB-6jgv: Crystal structure of the transcriptional regulator CadR from P. putida -

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Basic information

Entry
Database: PDB / ID: 6jgv
TitleCrystal structure of the transcriptional regulator CadR from P. putida
ComponentsCadR
KeywordsTRANSCRIPTION / CadR / MerR family / cadmium regulator
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 / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
A: CadR
B: CadR


Theoretical massNumber of molelcules
Total (without water)33,3432
Polymers33,3432
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-26 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.304, 47.304, 100.385
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
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: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 1 - 128 / Label seq-ID: 1 - 128

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 1.94 Å3/Da / Density % sol: 36.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 3350, magnesum chloride, Tris-HCl

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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: 2.2→30 Å / Num. obs: 12450 / % possible obs: 97.5 % / Redundancy: 5.9 % / Rsym value: 0.078 / Net I/σ(I): 21.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1228 / % possible all: 95.3

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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: 6JGF

6jgf


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.33 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.321 / ESU R Free: 0.228 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24983 630 5.1 %RANDOM
Rwork0.20766 ---
obs0.2099 11813 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 63.894 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0.3 Å2-0 Å2
2---0.6 Å2-0 Å2
3---1.94 Å2
Refinement stepCycle: 1 / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 0 25 1927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191916
X-RAY DIFFRACTIONr_bond_other_d0.0020.021880
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9842582
X-RAY DIFFRACTIONr_angle_other_deg0.9434298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2125232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8723.922102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56515362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7411524
X-RAY DIFFRACTIONr_chiral_restr0.0610.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022148
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02424
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_it3.9426.17946
X-RAY DIFFRACTIONr_mcbond_other3.9446.165945
X-RAY DIFFRACTIONr_mcangle_it5.9929.1891172
X-RAY DIFFRACTIONr_mcangle_other5.999.1951173
X-RAY DIFFRACTIONr_scbond_it4.5696.724970
X-RAY DIFFRACTIONr_scbond_other4.5666.727971
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4499.8921410
X-RAY DIFFRACTIONr_long_range_B_refined10.43847.4952158
X-RAY DIFFRACTIONr_long_range_B_other10.44247.5222155
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14314 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.03 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 50 -
Rwork0.269 870 -
obs--95.14 %

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