3DGE | pdb_00003dge

Structure of a histidine kinase-response regulator complex reveals insights into Two-component signaling and a novel cis-autophosphorylation mechanism

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	294	1.7M ammonium sulfate, 2.5% dioxane, 0.1M citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 183.958	α = 90
b = 90.668	β = 108.42
c = 68.985	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	MAR CCD 165 mm	mirror	2004-01-01	M	MAD
2	1	x-ray	110	CCD	ADSC QUANTUM 4	Toroidal mirror	2004-01-01	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM16	0.97935, 0.97950, 0.95298	ESRF	BM16
2	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.931	ESRF	ID14-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1,2	2.8	43.64	99.7	0.072	0.072	16.2	4.4	26588	116062		3	79

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.8	2.95	100		0.4	0.4	2.8	4.4	3875

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.8	43.64	25230	116062	1326	99.7	0.236	0.236	0.234	0.23	0.284	0.23	RANDOM	74.876

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-2.57		-0.84	3.78		-1.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.751
r_dihedral_angle_3_deg	22.017
r_dihedral_angle_4_deg	19.381
r_dihedral_angle_1_deg	6.508
r_scangle_it	3.491
r_scbond_it	2.373
r_angle_refined_deg	1.556
r_mcangle_it	1.544
r_mcbond_it	1.209
r_nbtor_refined	0.319

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.751
r_dihedral_angle_3_deg	22.017
r_dihedral_angle_4_deg	19.381
r_dihedral_angle_1_deg	6.508
r_scangle_it	3.491
r_scbond_it	2.373
r_angle_refined_deg	1.556
r_mcangle_it	1.544
r_mcbond_it	1.209
r_nbtor_refined	0.319
r_symmetry_vdw_refined	0.27
r_nbd_refined	0.258
r_symmetry_hbond_refined	0.219
r_xyhbond_nbd_refined	0.211
r_metal_ion_refined	0.184
r_chiral_restr	0.095
r_bond_refined_d	0.018
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5712
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	77

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
APEX	data collection
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.