[English] 日本語
Yorodumi
- PDB-6jyw: Crystal structure of the transcription regulator CadR N81M mutant... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jyw
TitleCrystal structure of the transcription regulator CadR N81M mutant from P. putida in complex with Cadmium(II) and DNA
Components
  • CadR
  • DNA (5'-D(*AP*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(*TP*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: 2.95 Å
AuthorsLiu, X.C. / Chen, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: To Be Published
Title: Crystal structure of the transcription regulator CadR N81M mutant from P. putida in complex with Cadmium(II) and DNA
Authors: Liu, X.C. / Chen, H.
History
DepositionApr 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CadR
B: CadR
C: DNA (5'-D(*AP*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(*TP*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)47,3318
Polymers46,8814
Non-polymers4504
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9880 Å2
ΔGint-104 kcal/mol
Surface area20300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.435, 126.435, 93.783
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

-
Components

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


Mass: 16688.799 Da / Num. of mol.: 2 / Mutation: N81M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: cadR, BIW19_10095, BL240_26950, EFK07_13565 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93TP7
#2: DNA chain DNA (5'-D(*AP*AP*CP*CP*CP*TP*AP*TP*AP*GP*TP*GP*GP*CP*TP*AP*CP*AP*GP*GP*GP*T)-3')


Mass: 6776.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas putida (bacteria)
#3: DNA chain DNA (5'-D(*TP*AP*CP*CP*CP*TP*GP*TP*AP*GP*CP*CP*AP*CP*TP*AP*TP*AP*GP*GP*GP*T)-3')


Mass: 6727.354 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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.62 Å3/Da / Density % sol: 73.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, sodium citrate tribasic dihydrate

-
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, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. obs: 17117 / % possible obs: 99.7 % / Redundancy: 6.3 % / Rsym value: 0.09 / Net I/σ(I): 20.1
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JGX

6jgx


Resolution: 2.95→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 14.192 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.475 / ESU R Free: 0.32 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25293 912 5.1 %RANDOM
Rwork0.20244 ---
obs0.20504 17117 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 90.174 Å2
Baniso -1Baniso -2Baniso -3
1--4.5 Å2-2.25 Å2-0 Å2
2---4.5 Å20 Å2
3---14.59 Å2
Refinement stepCycle: 1 / Resolution: 2.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2134 896 4 0 3034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0173159
X-RAY DIFFRACTIONr_bond_other_d0.0030.022542
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.6954452
X-RAY DIFFRACTIONr_angle_other_deg1.23535859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8485266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.94923.274113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.68715390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2571529
X-RAY DIFFRACTIONr_chiral_restr0.0730.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022975
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02710
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_it6.2289.0651079
X-RAY DIFFRACTIONr_mcbond_other6.2259.061078
X-RAY DIFFRACTIONr_mcangle_it9.38613.5621340
X-RAY DIFFRACTIONr_mcangle_other9.38213.5681341
X-RAY DIFFRACTIONr_scbond_it8.2629.2512080
X-RAY DIFFRACTIONr_scbond_other8.2629.2522079
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.76613.7533113
X-RAY DIFFRACTIONr_long_range_B_refined14.47475.2323864
X-RAY DIFFRACTIONr_long_range_B_other14.47675.2283863
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14698 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 53 -
Rwork0.373 1288 -
obs--99.78 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more