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- PDB-6dk8: RetS kinase region without cobalt -

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Basic information

Entry
Database: PDB / ID: 6dk8
TitleRetS kinase region without 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
NICKEL (II) ION / histidine kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 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 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RetS (Regulator of Exopolysaccharide and Type III Secretion)
B: 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)
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)206,60728
Polymers205,4338
Non-polymers1,17420
Water0
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)51,7108
Polymers51,3582
Non-polymers3526
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-72 kcal/mol
Surface area22610 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)51,5936
Polymers51,3582
Non-polymers2354
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-65 kcal/mol
Surface area22550 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)51,6527
Polymers51,3582
Non-polymers2935
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-67 kcal/mol
Surface area22660 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)51,6527
Polymers51,3582
Non-polymers2935
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-73 kcal/mol
Surface area22240 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: 25679.170 Da / Num. of mol.: 8 / Fragment: kinase domain (UNP residues 415-649)
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-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Ni

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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: 3.72 Å3/Da / Density % sol: 66.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.7 M sodium chloride, 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9739 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 21, 2016
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9739 Å / Relative weight: 1
ReflectionResolution: 3.8→56.78 Å / Num. obs: 31211 / % possible obs: 100 % / Redundancy: 26.2 % / CC1/2: 0.999 / Net I/σ(I): 8.1
Reflection shellResolution: 3.8→3.936 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DK7

6dk7


Resolution: 3.8→56.779 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 850 2.72 %
Rwork0.2146 30361 -
obs0.2155 31211 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.98 Å2 / Biso mean: 53.968 Å2 / Biso min: 8.52 Å2
Refinement stepCycle: final / Resolution: 3.8→56.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13847 0 20 0 13867
Biso mean--71.79 --
Num. residues----1791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314051
X-RAY DIFFRACTIONf_angle_d0.75419001
X-RAY DIFFRACTIONf_chiral_restr0.0422288
X-RAY DIFFRACTIONf_plane_restr0.0052486
X-RAY DIFFRACTIONf_dihedral_angle_d18.9978647
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.8-4.0380.31881380.240449725110100
4.038-4.34970.221410.213449965137100
4.3497-4.78720.22011390.18950165155100
4.7872-5.47950.27451400.207450425182100
5.4795-6.90160.29261430.267451135256100
6.9016-56.78520.20941490.19565222537198

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