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- PDB-6oap: Crystal structure of a dual sensor histidine kinase in the green-... -

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Basic information

Entry
Database: PDB / ID: 6oap
TitleCrystal structure of a dual sensor histidine kinase in the green-light absorbing Pg 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: 1.97 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 / struct_conn_type
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.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.conn_type_id / _struct_conn.id / _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 / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-87 kcal/mol
Surface area28450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.532, 72.532, 254.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-633-

HOH

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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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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 / pH: 7.5
Details: PEG 3350, magnesium chloride, HEPES. Crystals grown in dark

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 47992 / % possible obs: 97.2 % / Redundancy: 13 % / Biso Wilson estimate: 38.416150823 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.02 / Rrim(I) all: 0.074 / Χ2: 0.596 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.97-210.71.13923360.680.361.1970.40397.2
2-2.04121.0123450.8240.3011.0550.40397.6
2.04-2.0812.60.88823760.8660.2580.9250.41997.7
2.08-2.1213.30.71723510.9170.2010.7460.40897.7
2.12-2.1713.50.59423600.9450.1660.6170.41797.9
2.17-2.2213.40.4923930.9630.1370.5090.42897.9
2.22-2.2713.20.42523840.9690.120.4420.4498
2.27-2.3413.30.34423950.9790.0960.3570.42998.2
2.34-2.412.80.26423660.9840.0760.2750.43598.2
2.4-2.4811.80.20723620.9870.0620.2170.45397.2
2.48-2.5712.60.15121560.9940.0430.1570.45287.1
2.57-2.6714.10.14624020.9950.040.1520.4798.6
2.67-2.813.90.11424360.9970.0310.1180.49298.7
2.8-2.9413.90.0924220.9980.0250.0940.54598.8
2.94-3.1313.70.07324490.9990.020.0760.61398.9
3.13-3.3713.50.05924470.9990.0160.0610.75898.9
3.37-3.7113.30.05124830.9990.0140.0530.88199
3.71-4.2412.50.04525190.9990.0130.0470.98299
4.24-5.3512.10.0422890.9990.0120.0421.17889.3
5.35-5012.90.03827210.9990.0110.0391.21197.8
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W2Z, 4ZYL

3w2z

4zyl


Resolution: 1.97→36.266 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2375 2000 4.17 %
Rwork0.1818 --
obs0.1841 47964 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→36.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4895 0 90 296 5281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135140
X-RAY DIFFRACTIONf_angle_d1.3856983
X-RAY DIFFRACTIONf_dihedral_angle_d15.6181906
X-RAY DIFFRACTIONf_chiral_restr0.054790
X-RAY DIFFRACTIONf_plane_restr0.006915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9699-2.01920.33841390.28323206X-RAY DIFFRACTION97
2.0192-2.07380.33691410.25833226X-RAY DIFFRACTION98
2.0738-2.13480.31741410.24023248X-RAY DIFFRACTION98
2.1348-2.20370.30131410.223238X-RAY DIFFRACTION98
2.2037-2.28240.25531420.21373258X-RAY DIFFRACTION98
2.2824-2.37380.28431410.21723238X-RAY DIFFRACTION98
2.3738-2.48180.31561410.21713262X-RAY DIFFRACTION98
2.4818-2.61260.25621330.20493041X-RAY DIFFRACTION91
2.6126-2.77620.26871440.21633310X-RAY DIFFRACTION99
2.7762-2.99050.24061440.21133322X-RAY DIFFRACTION99
2.9905-3.29130.26251470.19763372X-RAY DIFFRACTION99
3.2913-3.76710.23961480.16763396X-RAY DIFFRACTION99
3.7671-4.74450.18241430.13963287X-RAY DIFFRACTION95
4.7445-36.27210.19391550.15463560X-RAY DIFFRACTION97
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)
14.32850.6579-0.41283.5364-0.41266.60520.0812-0.06660.41350.2031-0.02510.1498-0.6030.1065-0.01990.3008-0.027-0.00470.19380.0150.2491-15.6132-6.355311.9344
25.81611.6920.95323.7480.18165.05060.1712-0.0511-0.01220.0997-0.11940.15690.1609-0.0683-0.01160.3471-0.0158-0.06280.1773-0.03380.2559-3.2673-11.159737.4209
33.2250.017-1.02413.4328-0.35286.74490.0620.3361-0.4045-0.2848-0.10610.27370.4109-0.14290.03460.41690.0196-0.07730.1886-0.05630.3976-23.1669-48.71165.3065
43.5561.2911-0.02684.67341.01485.20280.0183-0.9312-0.74340.7024-0.006-0.09830.6021-0.0951-0.07680.59580.09180.08510.50060.25550.4802-24.0178-47.147943.5477
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 3:115))
2X-RAY DIFFRACTION2chain 'B' and ((resseq 3:115))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 155:308))
4X-RAY DIFFRACTION4chain 'B' and ((resseq 155:308))

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