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Basic information

Entry
Database: PDB / ID: 6ob8
TitleCrystal structure of a dual sensor histidine kinase in green light illuminated state
ComponentsDual sensor histidine kinase
KeywordsSIGNALING PROTEIN / Cyanobacteriochrome / photoreceptors / tandem sensors
Function / homologyPHYCOCYANOBILIN
Function and homology information
Biological species[Leptolyngbya] sp. JSC-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 19, 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 / struct_conn_type / struct_ncs_dom_lim
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_alt_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.ptnr1_symmetry / _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.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_alt_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_symmetry / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)73,8438
Polymers72,5682
Non-polymers1,2756
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-89 kcal/mol
Surface area28970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.059, 72.059, 253.804
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PROPROALAALAchain AAA2 - 3082 - 308
2GLNGLNHISHISchain BBB3 - 3113 - 311

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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-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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. Illuminated using green light at various temperature (100-293K)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 37588 / % possible obs: 99.9 % / Redundancy: 9.3 % / Biso Wilson estimate: 44.86 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.037 / Rrim(I) all: 0.111 / Χ2: 1.635 / Net I/σ(I): 8.3 / Num. measured all: 349196
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.197.61.2718320.6550.4941.3650.854100
2.19-2.238.81.19418270.7450.4261.270.878100
2.23-2.279.71.06118500.8380.3581.120.888100
2.27-2.329.80.89618480.8670.30.9450.901100
2.32-2.379.80.76818330.8730.2560.810.923100
2.37-2.429.70.66518470.8980.2230.7020.978100
2.42-2.489.80.56118540.9280.1880.5920.972100
2.48-2.559.80.42618350.9580.1430.451.049100
2.55-2.629.80.3618540.9640.1210.381.08100
2.62-2.719.70.31918450.9690.1070.3361.147100
2.71-2.819.70.24718620.9820.0830.2611.293100
2.81-2.929.70.20418750.9870.0690.2161.484100
2.92-3.059.60.17618510.9910.060.1861.78100
3.05-3.219.60.14518820.9910.050.1532.044100
3.21-3.419.50.1118970.9940.0380.1162.313100
3.41-3.689.40.08318830.9970.0280.0872.443100
3.68-4.059.10.07119120.9960.0250.0762.817100
4.05-4.638.60.0619410.9980.0220.0643.384100
4.63-5.838.70.05219580.9980.0180.0552.931100
5.83-507.90.04421020.9980.0170.0472.65898

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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: 2.3→41.498 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2514 1641 5.33 %
Rwork0.2084 29129 -
obs0.2108 30770 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 301.57 Å2 / Biso mean: 68.8995 Å2 / Biso min: 9.19 Å2
Refinement stepCycle: final / Resolution: 2.3→41.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4952 0 176 138 5266
Biso mean--148.12 57.98 -
Num. residues----614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01710330
X-RAY DIFFRACTIONf_angle_d1.1514062
X-RAY DIFFRACTIONf_chiral_restr0.0371586
X-RAY DIFFRACTIONf_plane_restr0.0051844
X-RAY DIFFRACTIONf_dihedral_angle_d15.6413848
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2674X-RAY DIFFRACTION14.238TORSIONAL
12B2674X-RAY DIFFRACTION14.238TORSIONAL
Refinement TLS params.Method: refined / Origin x: -28.837 Å / Origin y: -46.109 Å / Origin z: 53.547 Å
111213212223313233
T2.2194 Å2-0.7856 Å2-0.4589 Å2-3.0088 Å20.6613 Å2--0.2095 Å2
L0.3541 °2-0.5613 °2-0.4046 °2-2.2378 °2-0.9828 °2--4.6646 °2
S-0.1631 Å °-0.8056 Å °-0.0981 Å °0.584 Å °0.1703 Å °0.1804 Å °0.908 Å °0.1518 Å °0.0353 Å °
Refinement TLS groupSelection details: ( CHAIN B AND RESID 401:401 )

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