- PDB-2isz: Crystal structure of a two-domain IdeR-DNA complex crystal form I -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 2isz
Title
Crystal structure of a two-domain IdeR-DNA complex crystal form I
Components
(mbtA/mbtB operator strand ...) x 2
Iron-dependent repressor ideR
Keywords
TRANSCRIPTION/DNA / DNA-binding protein / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information
catechol-containing siderophore biosynthetic process / cobalt ion binding / cadmium ion binding / nickel cation binding / transition metal ion binding / peptidoglycan-based cell wall / ferrous iron binding / manganese ion binding / response to oxidative stress / protein dimerization activity ...catechol-containing siderophore biosynthetic process / cobalt ion binding / cadmium ion binding / nickel cation binding / transition metal ion binding / peptidoglycan-based cell wall / ferrous iron binding / manganese ion binding / response to oxidative stress / protein dimerization activity / iron ion binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / zinc ion binding / plasma membrane / cytoplasm Similarity search - Function
Diphteria toxin repressor, SH3 domain / Diphteria toxin repressor SH3 domain / FeoA domain / 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 / FeoA domain / 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 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
NICKEL (II) ION / DNA / DNA (> 10) / Iron-dependent repressor IdeR / Iron-dependent repressor IdeR Similarity search - Component
Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 28% PEG 3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
ID
Name
Crystal-ID
Sol-ID
1
PEG3350
1
1
2
ammoniumacetate
1
1
3
Bis-Tris
1
1
4
PEG3350
1
2
5
ammoniumacetate
1
2
6
Bis-Tris
1
2
-
Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0781 Å
Detector
Type: ADSC QUANTUM 315 / Detector: CCD
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.0781 Å / Relative weight: 1
Reflection
Av σ(I) over netI: 8.9 / Number: 65232 / Rmerge(I) obs: 0.075 / Χ2: 1.05 / D res high: 2.4 Å / D res low: 50 Å / Num. obs: 34892 / % possible obs: 90.4
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
5.17
50
98.5
1
0.043
1.035
4.1
5.17
97.7
1
0.05
1.04
3.58
4.1
97.5
1
0.061
1.05
3.26
3.58
97.4
1
0.086
1.055
3.02
3.26
97.5
1
0.122
1.039
2.85
3.02
97.8
1
0.169
1.076
2.7
2.85
95.4
1
0.211
1.065
2.59
2.7
86.8
1
0.254
1.059
2.49
2.59
74.7
1
0.286
1.018
2.4
2.49
60.7
1
0.296
1.001
Reflection
Resolution: 2.4→50 Å / Num. obs: 34892 / % possible obs: 90.4 % / Rmerge(I) obs: 0.075 / Χ2: 1.047 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)
Rmerge(I) obs
Num. unique all
Χ2
% possible all
2.4-2.49
0.296
2361
1.001
60.7
2.49-2.59
0.286
2852
1.018
74.7
2.59-2.7
0.254
3365
1.059
86.8
2.7-2.85
0.211
3670
1.065
95.4
2.85-3.02
0.169
3809
1.076
97.8
3.02-3.26
0.122
3745
1.039
97.5
3.26-3.58
0.086
3757
1.055
97.4
3.58-4.1
0.061
3767
1.05
97.5
4.1-5.17
0.05
3749
1.04
97.7
5.17-50
0.043
3817
1.035
98.5
-
Phasing
Phasing MR
Rfactor: 0.261 / Cor.coef. Fo:Fc: 0.835
Highest resolution
Lowest resolution
Rotation
3 Å
48.84 Å
Translation
3 Å
48.84 Å
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
MOLREP
phasing
REFMAC
5.2.0005
refinement
PDB_EXTRACT
2
dataextraction
HKL-2000
datacollection
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U8R
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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