- PDB-2ykf: Sensor region of a sensor histidine kinase -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 2ykf
Title
Sensor region of a sensor histidine kinase
Components
PROBABLE SENSOR HISTIDINE KINASE PDTAS
Keywords
TRANSFERASE / TWO-COMPONENT SYSTEM / GAF DOMAIN / PAS DOMAIN
Function / homology
Function and homology information
protein histidine kinase activity / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / protein autophosphorylation / protein kinase activity / ATP binding / cytoplasm Similarity search - Function
GAF domain / Histidine kinase PdtaS, GAF domain / Histidine kinase PdtaS, GAF domain superfamily / Histidine kinase PdtaS, GAF domain / Signal transduction histidine kinase, subgroup 2, dimerisation and phosphoacceptor domain / Histidine kinase / PAS domain / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase ...GAF domain / Histidine kinase PdtaS, GAF domain / Histidine kinase PdtaS, GAF domain superfamily / Histidine kinase PdtaS, GAF domain / Signal transduction histidine kinase, subgroup 2, dimerisation and phosphoacceptor domain / Histidine kinase / PAS domain / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 2
-
Sample preparation
Crystal
Density Matthews: 2.41 Å3/Da / Density % sol: 49.02 % / Description: NONE
Crystal grow
pH: 7.5 / Details: pH 7.5
-
Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
1
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
Wavelength
SYNCHROTRON
EMBL/DESY, HAMBURG
X12
1
0.9190, 0.9187, 0.9050
SYNCHROTRON
EMBL/DESY, HAMBURG
X11
2
0.8051
Detector
Type
ID
Detector
Details
MARRESEARCH
1
CCD
MIRRORS
MAR555 FLAT PANEL
2
IMAGE PLATE
MIRRORS
Radiation
ID
Monochromator
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
DOUBLECRYSTALSI(111)
MAD
M
x-ray
1
2
DOUBLECRYSTALSI(111)
MAD
M
x-ray
1
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.919
1
2
0.9187
1
3
0.905
1
4
0.8051
1
Reflection
Resolution: 2→19.5 Å / Num. obs: 21659 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.5
Reflection shell
Highest resolution: 2 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.5 / % possible all: 99.4
-
Processing
Software
Name
Version
Classification
REFMAC
5.5.0072
refinement
DENZO
datareduction
XDS
datareduction
SCALEPACK
datascaling
XSCALE
datascaling
Auto-Rickshaw
phasing
Refinement
Method to determine structure: OTHER Starting model: NONE Resolution: 2→19.5 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.735 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. BUT ARE NOT IN THE DEPOSITED COORDINATES.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23956
1024
4.7 %
RANDOM
Rwork
0.18777
-
-
-
obs
0.19021
20591
99.95 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK