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- PDB-4gkg: Crystal structure of the S-Helix Linker -

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Basic information

Entry
Database: PDB / ID: 4gkg
TitleCrystal structure of the S-Helix Linker
ComponentsC4-dicarboxylate transport sensor protein dctB
KeywordsSIGNALING PROTEIN / Signaling helix / Signal transduction
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / ATP binding / plasma membrane
Similarity search - Function
Signal transduction histidine kinase, DctB (C4-dicarboxylate transport system regulator) / Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / 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 ...Signal transduction histidine kinase, DctB (C4-dicarboxylate transport system regulator) / Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / 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. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / C4-dicarboxylate transport sensor protein DctB
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.695 Å
AuthorsLiu, J.W. / Lu, D. / Sun, Y.J. / Wen, J. / Yang, Y. / Yang, J.G. / Wei, X.L. / Zhang, X.D. / Wang, Y.P.
CitationJournal: To be Published
Title: Crystal structure of the S-Helix Linker
Authors: Liu, J.W. / Lu, D. / Sun, Y.J. / Wen, J. / Yang, Y. / Yang, J.G. / Wei, X.L. / Zhang, X.D. / Wang, Y.P.
History
DepositionAug 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C4-dicarboxylate transport sensor protein dctB
F: C4-dicarboxylate transport sensor protein dctB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8385
Polymers15,5532
Non-polymers2853
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-35 kcal/mol
Surface area8400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.960, 40.960, 302.421
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein C4-dicarboxylate transport sensor protein dctB


Mass: 7776.606 Da / Num. of mol.: 2 / Fragment: cytoplasmic linker
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: dctB, RB1524, SMb20612 / Plasmid: pET28a-S-Helix / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13633, histidine kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 8-12% PEG1500, 15-20% Isopropanol, 100mM Sodium Citrate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0210.9795, 1.07210, 1.05830
SYNCHROTRONDiamond I0320.9795, 1.07210, 1.05830
Detector
TypeIDDetector
ADSC QUANTUM 3151CCD
ADSC QUANTUM 3152CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.07211
31.05831
ReflectionResolution: 1.695→50.613 Å / Num. obs: 18052

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Standard 7 amino acid helix

Resolution: 1.695→34.535 Å / SU ML: 0.42 / σ(F): 1.1 / Phase error: 30 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2759 1605 5.16 %
Rwork0.2364 --
obs0.2383 31108 98.76 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.228 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.0102 Å2-0 Å2-0 Å2
2--12.0102 Å2-0 Å2
3----24.0205 Å2
Refinement stepCycle: LAST / Resolution: 1.695→34.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms789 0 15 74 878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01816
X-RAY DIFFRACTIONf_angle_d1.1181096
X-RAY DIFFRACTIONf_dihedral_angle_d17.375327
X-RAY DIFFRACTIONf_chiral_restr0.07124
X-RAY DIFFRACTIONf_plane_restr0.004146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.695-1.74970.41331500.34892642X-RAY DIFFRACTION99
1.7497-1.81220.32471750.29862693X-RAY DIFFRACTION99
1.8122-1.88480.29011140.27482726X-RAY DIFFRACTION99
1.8848-1.97060.37191580.25322722X-RAY DIFFRACTION99
1.9706-2.07440.27881540.2592676X-RAY DIFFRACTION100
2.0744-2.20440.21771750.21032695X-RAY DIFFRACTION100
2.2044-2.37460.23771420.19042715X-RAY DIFFRACTION100
2.3746-2.61340.29061290.21412709X-RAY DIFFRACTION100
2.6134-2.99140.23811250.21932737X-RAY DIFFRACTION100
2.9914-3.76820.29991380.21682737X-RAY DIFFRACTION100
3.7682-34.54190.26541450.26492451X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.32830.36783.02972.2095-2.59328.42840.1625-0.54690.34660.5483-0.4425-0.8232-0.5167-1.36360.38250.2953-0.05610.03380.7019-0.08310.42683.7687-8.564684.7638
2-0.8250.57081.7518-0.22170.69268.02080.1592-0.1055-0.0341-0.1897-0.0918-0.0051-0.0567-0.266-0.05060.32060.1712-0.00030.548-0.02340.35780.3245-12.346652.9767
34.5899-0.13623.52187.6186-4.28615.0097-0.03010.6005-0.95780.00150.2794-0.22662.26070.9129-0.21750.62280.0943-0.07490.3607-0.03670.4068-4.4124-20.826120.5889
40.9430.8391-1.17632.21360.6493.68580.0787-0.10880.119-0.1908-0.0611-0.1279-0.57181.4925-0.07530.32540.3057-0.02310.3441-0.09240.39846.9935-15.315137.0735
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 344:348)
2X-RAY DIFFRACTION2chain 'A' and (resseq 349:386)
3X-RAY DIFFRACTION3chain 'A' and (resseq 387:395)
4X-RAY DIFFRACTION4chain 'F'

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