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- PDB-6dk7: RetS histidine kinase region with cobalt -

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Basic information

Entry
Database: PDB / ID: 6dk7
TitleRetS histidine kinase region with cobalt
ComponentsRetS (Regulator of Exopolysaccharide and Type III Secretion)Type three secretion system
KeywordsSIGNALING PROTEIN / Histidine kinase / Inhibitor
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / membrane
Similarity search - Function
7TM-DISM receptor, extracellular domain, type 2 / 7TM-DISM receptor, extracellular domain, type 1 / 7TM diverse intracellular signalling / 7TMR-DISM extracellular 2 / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain ...7TM-DISM receptor, extracellular domain, type 2 / 7TM-DISM receptor, extracellular domain, type 1 / 7TM diverse intracellular signalling / 7TMR-DISM extracellular 2 / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
: / histidine kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsMancl, J.M. / Schubot, F.D.
CitationJournal: Structure / Year: 2019
Title: Helix Cracking Regulates the Critical Interaction between RetS and GacS in Pseudomonas aeruginosa.
Authors: Mancl, J.M. / Ray, W.K. / Helm, R.F. / Schubot, F.D.
History
DepositionMay 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.3May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first
Revision 1.4Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RetS (Regulator of Exopolysaccharide and Type III Secretion)
C: RetS (Regulator of Exopolysaccharide and Type III Secretion)
D: RetS (Regulator of Exopolysaccharide and Type III Secretion)
B: RetS (Regulator of Exopolysaccharide and Type III Secretion)
E: RetS (Regulator of Exopolysaccharide and Type III Secretion)
F: RetS (Regulator of Exopolysaccharide and Type III Secretion)
G: RetS (Regulator of Exopolysaccharide and Type III Secretion)
H: RetS (Regulator of Exopolysaccharide and Type III Secretion)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,81732
Polymers199,4038
Non-polymers1,41424
Water4,504250
1
A: RetS (Regulator of Exopolysaccharide and Type III Secretion)
B: RetS (Regulator of Exopolysaccharide and Type III Secretion)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2048
Polymers49,8512
Non-polymers3546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-78 kcal/mol
Surface area22220 Å2
MethodPISA
2
C: RetS (Regulator of Exopolysaccharide and Type III Secretion)
D: RetS (Regulator of Exopolysaccharide and Type III Secretion)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2639
Polymers49,8512
Non-polymers4137
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-76 kcal/mol
Surface area22400 Å2
MethodPISA
3
E: RetS (Regulator of Exopolysaccharide and Type III Secretion)
F: RetS (Regulator of Exopolysaccharide and Type III Secretion)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2048
Polymers49,8512
Non-polymers3546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-76 kcal/mol
Surface area22310 Å2
MethodPISA
4
G: RetS (Regulator of Exopolysaccharide and Type III Secretion)
H: RetS (Regulator of Exopolysaccharide and Type III Secretion)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1457
Polymers49,8512
Non-polymers2955
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-75 kcal/mol
Surface area22540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.708, 158.708, 243.826
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
RetS (Regulator of Exopolysaccharide and Type III Secretion) / Type three secretion system


Mass: 24925.367 Da / Num. of mol.: 8 / Fragment: kinase domain (UNP residues 416-649)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: retS, PA4856 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HUV7
#2: Chemical...
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Formula: Co
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 3.89 Å3/Da / Density % sol: 68.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: sodium chloride, HEPES, cobalt chloride

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS-II 17-ID-110.97881, 0.9751
SYNCHROTRONAPS 31-ID20.97931
Detector
TypeIDDetectorDate
DECTRIS EIGER X 9M1PIXELAug 4, 2017
RAYONIX MX225HE2CCDFeb 29, 2016
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)MADMx-ray1
2diamond(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978811
20.97511
30.979311
ReflectionResolution: 2.6→56.89 Å / Num. obs: 96240 / % possible obs: 99.9 % / Redundancy: 14.3 % / CC1/2: 0.997 / Net I/σ(I): 9.3
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.7454 / Num. unique obs: 13834 / CC1/2: 0.273 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
SCALAdata scaling
PHENIXphasing
xia2data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.6→56.779 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 28.22
RfactorNum. reflection% reflection
Rfree0.2606 2519 2.72 %
Rwork0.211 --
obs0.2123 92477 96.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 145.27 Å2 / Biso mean: 61.6017 Å2 / Biso min: 16.92 Å2
Refinement stepCycle: final / Resolution: 2.6→56.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13864 0 24 250 14138
Biso mean--87.39 53.45 -
Num. residues----1795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614088
X-RAY DIFFRACTIONf_angle_d0.83819053
X-RAY DIFFRACTIONf_chiral_restr0.0462291
X-RAY DIFFRACTIONf_plane_restr0.0052495
X-RAY DIFFRACTIONf_dihedral_angle_d16.4648669
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.650.39181110.3484017412879
2.65-2.70410.35821280.32664424455286
2.7041-2.76290.3261210.30554669479091
2.7629-2.82720.33051320.30164777490993
2.8272-2.89790.32741370.2994876501395
2.8979-2.97620.39091430.30334957510097
2.9762-3.06380.32851430.27125074521798
3.0638-3.16270.32891430.24985090523399
3.1627-3.27570.31411420.24555076521899
3.2757-3.40680.27761440.22965135527999
3.4068-3.56190.24441450.21575133527899
3.5619-3.74960.22591440.195651435287100
3.7496-3.98450.26381460.179951835329100
3.9845-4.2920.23441450.168751935338100
4.292-4.72380.20251460.151452195365100
4.7238-5.40680.21691460.17152435389100
5.4068-6.81020.26361480.22253105458100
6.8102-56.79240.21641550.1785439559498

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