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- PDB-6oaq: Crystal structure of a dual sensor histidine kinase in BeF3- boun... -

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Basic information

Entry
Database: PDB / ID: 6oaq
TitleCrystal structure of a dual sensor histidine kinase in BeF3- bound state
ComponentsDual sensor histidine kinase
KeywordsSIGNALING PROTEIN / Cyanobacteriochrome / photoreceptors / tandem sensors
Function / homologyBERYLLIUM TRIFLUORIDE ION / PHYCOCYANOBILIN
Function and homology information
Biological species[Leptolyngbya] sp. JSC-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsHeewhan, S. / Zhong, R. / Xiaoli, Z. / Sepalika, B. / Xiaojing, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01EY024363 United States
Other privateCBC C-086 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structural basis of molecular logic OR in a dual-sensor histidine kinase.
Authors: Shin, H. / Ren, Z. / Zeng, X. / Bandara, S. / Yang, X.
History
DepositionMar 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dual sensor histidine kinase
B: Dual sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9099
Polymers72,5682
Non-polymers1,3417
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-76 kcal/mol
Surface area28180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.526, 73.526, 253.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Dual sensor histidine kinase


Mass: 36284.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Leptolyngbya] sp. JSC-1 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, magnesium chloride, HEPES, Crystals grown in dark, Soaked in phosphorylation mimic solution containing BeSO4, NaF, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 21951 / % possible obs: 99.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.034 / Rrim(I) all: 0.088 / Χ2: 1.584 / Net I/σ(I): 28.54
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 6 % / Rmerge(I) obs: 1.108 / Num. unique obs: 1790 / Rpim(I) all: 0.611 / Rrim(I) all: 0.45 / % possible all: 81.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W2Z, 4ZYL

3w2z

4zyl


Resolution: 2.54→44.285 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2407 1914 9.14 %
Rwork0.1908 --
obs0.1955 20930 87.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.54→44.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4861 0 94 52 5007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035064
X-RAY DIFFRACTIONf_angle_d0.9476890
X-RAY DIFFRACTIONf_dihedral_angle_d14.7531885
X-RAY DIFFRACTIONf_chiral_restr0.026779
X-RAY DIFFRACTIONf_plane_restr0.004901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.60350.36621260.30521252X-RAY DIFFRACTION83
2.6035-2.67390.31311240.2861231X-RAY DIFFRACTION82
2.6739-2.75260.2811250.26521244X-RAY DIFFRACTION82
2.7526-2.84140.29371260.24791249X-RAY DIFFRACTION82
2.8414-2.9430.33131270.25041254X-RAY DIFFRACTION81
2.943-3.06080.31781260.26911262X-RAY DIFFRACTION82
3.0608-3.20.34471260.24251258X-RAY DIFFRACTION83
3.2-3.36870.29211290.22841271X-RAY DIFFRACTION83
3.3687-3.57970.26191320.21231314X-RAY DIFFRACTION85
3.5797-3.85590.26071390.19991381X-RAY DIFFRACTION89
3.8559-4.24370.24271460.17611458X-RAY DIFFRACTION94
4.2437-4.85710.19581550.14811529X-RAY DIFFRACTION96
4.8571-6.11680.22041610.17631605X-RAY DIFFRACTION99
6.1168-44.29160.19511720.16321708X-RAY DIFFRACTION99
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)
17.1610.6381-0.9146.1182-0.65186.60330.06190.05810.33560.191-0.00050.2069-0.48970.0376-0.08010.5248-0.0097-0.05870.380.09040.3639-15.8905-6.841912.0715
23.17160.8127-0.77685.66-1.93848.53160.21370.6085-0.4775-0.2796-0.20290.28550.70970.05780.06780.58170.1292-0.08310.4797-0.12180.5296-23.4485-48.81745.6445
38.05970.7768-0.28424.29330.76266.17650.4202-0.14210.05060.2028-0.3590.18250.118-0.2786-0.06930.5377-0.0393-0.08020.423-0.03220.4069-3.0024-11.61437.4989
42.97370.5147-0.77475.0810.86917.0435-0.0409-0.6306-0.62840.8782-0.02060.04760.94220.0472-0.02990.8510.13090.07120.64010.2370.6461-24.2871-47.122743.7037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:115 )A3 - 115
2X-RAY DIFFRACTION2( CHAIN A AND RESID 155:308 )A155 - 308
3X-RAY DIFFRACTION3( CHAIN B AND RESID 3:115 )B3 - 115
4X-RAY DIFFRACTION4( CHAIN B AND RESID 155:307 )B155 - 307

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