- PDB-3no0: Aquifex aeolicus type IIA topoisomerase C-terminal domain -
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Basic information
Entry
Database: PDB / ID: 3no0
Title
Aquifex aeolicus type IIA topoisomerase C-terminal domain
Components
DNA gyrase subunit A
Keywords
ISOMERASE / DNA topology / topoisomerase / Aquifex aeolicus / C-terminal domain / gyrase / DNA binding protein
Function / homology
Function and homology information
DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA binding / ATP binding / cytoplasm Similarity search - Function
DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA-like domain superfamily ...DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA-like domain superfamily / 6 Propeller / Neuraminidase / Mainly Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 948 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE UNP SEQUENCE FOR THIS ENTRY TERMINATES PREMATURELY DUE TO A SEQUENCE FRAME SHIFT. THE CORRECT C- ...THE UNP SEQUENCE FOR THIS ENTRY TERMINATES PREMATURELY DUE TO A SEQUENCE FRAME SHIFT. THE CORRECT C-TERMINUS SEQUENCE CONTINUES WITH DKINQKDIPLSTKKSIPRTRWKLEDDEIIKVVIKKSE
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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
ID
Density Matthews (Å3/Da)
Density % sol (%)
1
2.54
51.5
2
3
4
Crystal grow
Temperature (K)
Crystal-ID
Method
pH
Details
291
1
vapor diffusion, hanging drop
7.5
50 mM NaCL, 10mM Tris-HCl pH 7.5, 225 mM NH4NO3, 20% PEG 3500, VAPOR DIFFUSION, HANGING DROP, temperature 291K
291
2
vapor diffusion, hanging drop
7.5
50 mM NaCL, 10mM Tris-HCl pH 7.5, 50mM NaNO3, 20% PEG 3500, 10mM K2Pt(CN4), VAPOR DIFFUSION, HANGING DROP, temperature 291K
291
3
vapor diffusion, hanging drop
7.5
50 mM NaCL, 10mM Tris-HCl pH 7.5, 50mM NaNO3, 20% PEG 3500, 10 mM K2PtCl4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
291
4
vapor diffusion, hanging drop
7.5
50 mM NaCL, 10mM Tris-HCl pH 7.5, 50mM NaNO3, 20% PEG 3500, 10 mM NaWO4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
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Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
1
3
100
1
4
100
1
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
SYNCHROTRON
ALS
8.3.1
1
1.1
SYNCHROTRON
ALS
8.3.1
2
1.071
SYNCHROTRON
ALS
8.3.1
3
1.071
SYNCHROTRON
ALS
8.3.1
4
1.214
Detector
Type
ID
Detector
Date
ADSC QUANTUM 315r
1
CCD
Apr 20, 2007
ADSC QUANTUM 315r
2
CCD
May 9, 2007
ADSC QUANTUM 315r
3
CCD
May 9, 2007
ADSC QUANTUM 315r
4
CCD
May 9, 2007
Radiation
ID
Monochromator
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
Doubleflatcrystal, Si(111)
SINGLEWAVELENGTH
M
x-ray
1
2
Doubleflatcrystal, Si(111)
SINGLEWAVELENGTH
M
x-ray
1
3
Doubleflatcrystal, Si(111)
SINGLEWAVELENGTH
M
x-ray
1
4
Doubleflatcrystal, Si(111)
SINGLEWAVELENGTH
M
x-ray
1
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
1.1
1
2
1.071
1
3
1.214
1
Reflection
Resolution: 1.3→40.851 Å / Num. all: 222500 / Num. obs: 208073 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 15.36 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 28.2
Reflection shell
Resolution: 1.3→1.315 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.4 / Num. unique all: 18736 / % possible all: 84.8
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Processing
Software
Name
Version
Classification
HKL-2000
datacollection
SOLVE
phasing
PHENIX
(phenix.refine: 1.5_2)
refinement
HKL-2000
datareduction
SCALA
datascaling
Refinement
Method to determine structure: MIRAS / Resolution: 1.3004→40.851 Å / SU ML: 0.2 / Phase error: 18.05 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1894
10451
5.02 %
random, 5%
Rwork
0.1725
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-
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obs
0.1734
208073
93.51 %
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all
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222500
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Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.454 Å2 / ksol: 0.354 e/Å3