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- PDB-3hcy: The crystal structure of the domain of putative two-component sen... -

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Basic information

Entry
Database: PDB / ID: 3hcy
TitleThe crystal structure of the domain of putative two-component sensor histidine kinase protein from Sinorhizobium meliloti 1021
ComponentsPutative two-component sensor histidine kinase protein
Keywordsstructural genomics / unknown function / Two-component sensor histidine kinase protein / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / Kinase
Function / homology
Function and homology information


protein histidine kinase activity / histidine kinase / regulation of DNA-templated transcription / ATP binding
Similarity search - Function
Signal transduction histidine kinase, HWE region / HWE histidine kinase / HWE histidine kinase / GAF domain / PAS fold-4 / PAS fold / PAS fold-3 / PAS fold / GAF domain / PAS domain ...Signal transduction histidine kinase, HWE region / HWE histidine kinase / HWE histidine kinase / GAF domain / PAS fold-4 / PAS fold / PAS fold-3 / PAS fold / GAF domain / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Blue-light-activated histidine kinase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsZhang, R. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the domain of putative two-component sensor histidine kinase protein from Sinorhizobium meliloti 1021
Authors: Zhang, R. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMay 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative two-component sensor histidine kinase protein
B: Putative two-component sensor histidine kinase protein


Theoretical massNumber of molelcules
Total (without water)33,8182
Polymers33,8182
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-11 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.346, 73.346, 257.258
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThis protein exists as dimer. The deposited MolA and MolB represent the dimer in the asymmetric unit.

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Components

#1: Protein Putative two-component sensor histidine kinase protein


Mass: 16908.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: exsG, GI:16264804, RB1056, SMb20933, SM_b20933 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q92UP1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Sodium Acetate, 2.0M Sodium Formate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794, 0.9796
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2008 / Details: Si 111 channel
RadiationMonochromator: mirror / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
ReflectionResolution: 2.8→61.66 Å / Num. all: 10343 / Num. obs: 10322 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 25.7 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 30.2
Reflection shellResolution: 2.8→2.873 Å / Redundancy: 24.5 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 3.38 / Num. unique all: 774 / % possible all: 99.1

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SOLVEphasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→61.66 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.894 / SU B: 34.245 / SU ML: 0.297 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.796 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26018 523 4.8 %RANDOM
Rwork0.20674 ---
obs0.20969 10322 99.8 %-
all-10343 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.36 Å2
Baniso -1Baniso -2Baniso -3
1--2.12 Å2-1.06 Å20 Å2
2---2.12 Å20 Å2
3---3.18 Å2
Refinement stepCycle: LAST / Resolution: 2.8→61.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 0 12 2266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222298
X-RAY DIFFRACTIONr_bond_other_d0.0020.021560
X-RAY DIFFRACTIONr_angle_refined_deg2.0521.953103
X-RAY DIFFRACTIONr_angle_other_deg1.12833755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.7385285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.42123.445119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.72715368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4741521
X-RAY DIFFRACTIONr_chiral_restr0.1220.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02511
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9391.51428
X-RAY DIFFRACTIONr_mcbond_other0.1411.5588
X-RAY DIFFRACTIONr_mcangle_it1.79322266
X-RAY DIFFRACTIONr_scbond_it2.4183870
X-RAY DIFFRACTIONr_scangle_it4.1014.5837
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 40 -
Rwork0.283 727 -
obs-767 99.1 %
Refinement TLS params.Method: refined / Origin x: 26.486 Å / Origin y: 19.81 Å / Origin z: 131.66 Å
111213212223313233
T0.3195 Å20.0075 Å2-0.0401 Å2-0.1678 Å20.0847 Å2--0.21 Å2
L3.0295 °2-0.101 °21.5506 °2-0.9359 °2-0.6812 °2--1.9028 °2
S0.1681 Å °-0.1222 Å °-0.2593 Å °-0.2096 Å °0.0248 Å °0.0058 Å °0.2053 Å °0.0619 Å °-0.1929 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 145
2X-RAY DIFFRACTION1B-2 - 146

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