- PDB-2it0: Crystal structure of a two-domain IdeR-DNA complex crystal form II -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2it0
Title
Crystal structure of a two-domain IdeR-DNA complex crystal form II
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
ACETATE ION / NICKEL (II) ION / DNA / DNA (> 10) / Iron-dependent repressor IdeR / Iron-dependent repressor IdeR Similarity search - Component
Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.97 Å3/Da / Density % sol: 58.52 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 26% PEG 4000, 0.2 M sodium acetate, 0.1 M Tris HCl pH 8.5, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
ID
Name
Crystal-ID
Sol-ID
1
PEG4000
1
1
2
Naacetate
1
1
3
TrisHCl
1
1
4
PEG4000
1
2
5
Naacetate
1
2
6
TrisHCl
1
2
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1217 Å
Detector
Type: ADSC QUANTUM 315 / Detector: CCD
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.1217 Å / Relative weight: 1
Reflection
Redundancy: 1.9 % / Av σ(I) over netI: 3.8 / Number: 59087 / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / D res high: 2.6 Å / D res low: 72.481 Å / Num. obs: 31514 / % possible obs: 96.3
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Rsym value
Redundancy
8.22
37.91
97.2
1
0.053
0.053
1.9
5.81
8.22
98.1
1
0.055
0.055
2
4.75
5.81
96
1
0.151
0.151
1.6
4.11
4.75
96.2
1
0.082
0.082
1.8
3.68
4.11
96.1
1
0.063
0.063
1.9
3.36
3.68
96.5
1
0.087
0.087
1.9
3.11
3.36
96.5
1
0.108
0.108
1.9
2.91
3.11
96.3
1
0.207
0.207
1.9
2.74
2.91
96
1
0.263
0.263
1.9
2.6
2.74
95.9
1
0.348
0.348
1.9
Reflection
Resolution: 2.6→72.481 Å / Num. obs: 31514 / % possible obs: 96.3 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / Net I/σ(I): 3.8
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.6-2.74
1.9
0.348
2
8746
4585
0.348
95.9
2.74-2.91
1.9
0.263
2.8
8272
4345
0.263
96
2.91-3.11
1.9
0.207
3.5
7788
4093
0.207
96.3
3.11-3.36
1.9
0.108
6.8
7229
3821
0.108
96.5
3.36-3.68
1.9
0.087
7.9
6543
3493
0.087
96.5
3.68-4.11
1.9
0.063
11.1
5990
3188
0.063
96.1
4.11-4.75
1.8
0.082
7.9
5062
2786
0.082
96.2
4.75-5.81
1.6
0.151
2.2
3862
2346
0.151
96
5.81-8.22
2
0.055
13.2
3635
1850
0.055
98.1
8.22-37.91
1.9
0.053
10.3
1960
1007
0.053
97.2
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Phasing
Phasing MR
Rfactor: 0.354 / Cor.coef. Fo:Fc: 0.701
Highest resolution
Lowest resolution
Rotation
3 Å
37.91 Å
Translation
3 Å
37.91 Å
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Processing
Software
Name
Version
Classification
NB
SCALA
datascaling
MOLREP
phasing
REFMAC
5.2.0005
refinement
PDB_EXTRACT
2
dataextraction
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ISZ
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