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- PDB-3by8: Crystal Structure of the E.coli DcuS Sensor Domain -

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Basic information

Entry
Database: PDB / ID: 3by8
TitleCrystal Structure of the E.coli DcuS Sensor Domain
ComponentsSensor protein dcuS
KeywordsTRANSFERASE / histidine kinase sensor domain / Inner membrane / Membrane / Phosphoprotein / Transmembrane / Two-component regulatory system
Function / homology
Function and homology information


protein histidine kinase complex / protein histidine kinase activity / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / outer membrane-bounded periplasmic space / regulation of DNA-templated transcription / signal transduction / ATP binding / identical protein binding ...protein histidine kinase complex / protein histidine kinase activity / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / outer membrane-bounded periplasmic space / regulation of DNA-templated transcription / signal transduction / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
SpoOB, alpha-helical domain / Sensor_kinase_SpoOB-type, alpha-helical domain / Single cache domain 3 / Single cache domain 3 / Signal transduction histidine kinase, sporulation regulator SpoOB / Periplasmic sensor-like domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. ...SpoOB, alpha-helical domain / Sensor_kinase_SpoOB-type, alpha-helical domain / Single cache domain 3 / Single cache domain 3 / Signal transduction histidine kinase, sporulation regulator SpoOB / Periplasmic sensor-like domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
(2S)-2-hydroxybutanedioic acid / Sensor histidine kinase DcuS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsCheung, J. / Hendrickson, W.A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal Structures of C4-Dicarboxylate Ligand Complexes with Sensor Domains of Histidine Kinases DcuS and DctB.
Authors: Cheung, J. / Hendrickson, W.A.
History
DepositionJan 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 2.0Apr 21, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_ref_seq_dif / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Feb 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

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Assembly

Deposited unit
A: Sensor protein dcuS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8922
Polymers15,7581
Non-polymers1341
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Sensor protein dcuS
hetero molecules

A: Sensor protein dcuS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7844
Polymers31,5162
Non-polymers2682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.111, 86.111, 35.207
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Sensor protein dcuS


Mass: 15757.835 Da / Num. of mol.: 1 / Fragment: residues 42-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dcuS, yjdH / Plasmid: pGEX4T2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AEC8, histidine kinase
#2: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.5
Details: PEG MME 2000, isopropanol, ammonium citrate, pH 4.5, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9678, 0.9787, 0.9793, 0.9918
DetectorDetector: CCD / Date: Apr 7, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96781
20.97871
30.97931
40.99181
ReflectionAv σ(I) over netI: 9.6 / Number: 116612 / Rmerge(I) obs: 0.076 / Χ2: 1.03 / D res high: 2 Å / D res low: 30 Å / Num. obs: 19869 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.313098.410.0371.011
3.424.3199.710.0421.024
2.993.4299.910.0611.031
2.712.9999.910.091.039
2.522.7110010.1141.049
2.372.5299.910.1431.056
2.252.3710010.1841.022
2.152.2510010.2240.998
2.072.1510010.2831.047
22.0710010.3411.017
ReflectionResolution: 1.4→30 Å / Num. obs: 29824 / % possible obs: 99.9 % / Rmerge(I) obs: 0.046 / Χ2: 1.013 / Net I/σ(I): 17
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.4-1.450.23829500.98298.9
1.45-1.510.20329371.02499.9
1.51-1.580.15229531.027100
1.58-1.660.11329821.031100
1.66-1.760.08329441.014100
1.76-1.90.05929631100
1.9-2.090.04429771.007100
2.09-2.390.03630061.003100
2.39-3.020.05829991.013100
3.02-300.04131131.012100

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Phasing

Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 29802
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.62-10046.10.861511
4.4-5.6245.10.936508
3.81-4.444.80.941552
3.4-3.8146.40.924609
3.11-3.451.60.911659
2.87-3.1148.70.902735
2.69-2.8747.60.905773
2.53-2.6946.80.912815
2.4-2.5351.30.91881
2.29-2.452.60.911916
2.19-2.2960.30.902932
2.11-2.1964.90.9061003
2.03-2.1165.50.9011046
1.96-2.0381.60.9041046
1.9-1.9689.90.8991122
1.84-1.990.90.8951134
1.79-1.8489.80.8871153
1.74-1.7987.90.8821217
1.7-1.7491.40.8871224
1.66-1.790.10.8921260
1.62-1.6687.10.8741283
1.58-1.6291.20.8781320
1.55-1.5888.30.8871345
1.52-1.5589.20.8781371
1.49-1.5292.20.8721418
1.46-1.4988.90.8391402
1.43-1.4689.30.8341477
1.4-1.4390.80.7172090

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
DM4phasing
CNS1.1refinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.45→28.19 Å / Rfactor Rfree error: 0.006 / FOM work R set: 0.836 / Data cutoff high absF: 1110909.875 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1351 5 %RANDOM
Rwork0.219 ---
obs-26860 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.772 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å21.82 Å20 Å2
2--2.4 Å20 Å2
3----4.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.45→28.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1150 0 9 152 1311
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d1.26
X-RAY DIFFRACTIONc_mcbond_it1.761.5
X-RAY DIFFRACTIONc_mcangle_it2.62
X-RAY DIFFRACTIONc_scbond_it2.572
X-RAY DIFFRACTIONc_scangle_it3.812.5
LS refinement shellResolution: 1.45→1.54 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 226 5.1 %
Rwork0.261 4212 -
all-4438 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.parammal_xplor_top.txt
X-RAY DIFFRACTION3mal_xplor_par.txtwater.top

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