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- PDB-6uv8: Crystal structure of a far-red cyanobacteriochrome photoreceptor ... -

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Basic information

Entry
Database: PDB / ID: 6uv8
TitleCrystal structure of a far-red cyanobacteriochrome photoreceptor at room temperature
ComponentsMulti-sensor signal transduction histidine kinase
KeywordsSIGNALING PROTEIN / Photoreceptor / bilin-binding protein / far-red light
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity
Similarity search - Function
PAS fold-3 / PAS fold / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAC motif ...PAS fold-3 / PAS fold / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Domain in cystathionine beta-synthase and other proteins. / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / histidine kinase
Similarity search - Component
Biological speciesAnabaena cylindrica
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsYang, X. / Ren, Z. / Bandara, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01 EY024363 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Crystal structure of a far-red-sensing cyanobacteriochrome reveals an atypical bilin conformation and spectral tuning mechanism.
Authors: Bandara, S. / Rockwell, N.C. / Zeng, X. / Ren, Z. / Wang, C. / Shin, H. / Martin, S.S. / Moreno, M.V. / Lagarias, J.C. / Yang, X.
History
DepositionNov 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 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

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Assembly

Deposited unit
A: Multi-sensor signal transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6452
Polymers22,0561
Non-polymers5891
Water1448
1
A: Multi-sensor signal transduction histidine kinase
hetero molecules

A: Multi-sensor signal transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2894
Polymers44,1122
Non-polymers1,1772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/21
Buried area5130 Å2
ΔGint-56 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.800, 108.800, 67.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222

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Components

#1: Protein Multi-sensor signal transduction histidine kinase


Mass: 22056.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena cylindrica (strain ATCC 27899 / PCC 7122) (bacteria)
Strain: ATCC 27899 / PCC 7122 / Gene: Anacy_2551 / Production host: Escherichia coli (E. coli) / References: UniProt: K9ZI18
#2: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 4.56 Å3/Da / Density % sol: 73 %
Crystal growTemperature: 297 K / Method: batch mode / pH: 5.5
Details: 2 mg/mL protein, 8.5-10.5% polyethylene glycol 10,000 (PEG), 50 mM NH4CH3COO, and 50 mM Bis-tris buffer at pH 5.5

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Data collection

DiffractionMean temperature: 297 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.98-1.2
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 12, 2018
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
21.21
ReflectionResolution: 2.7→50 Å / Num. obs: 8453 / % possible obs: 98.7 % / Redundancy: 10.3 % / Biso Wilson estimate: 66.58 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 43.4
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.746 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 397 / % possible all: 99.8
Serial crystallography sample deliveryDescription: crystal-on-crystal device / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: crystal-on-crystal device / Motion control: inSituX
Serial crystallography data reductionFrames total: 800

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
Precognitiondata reduction
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GLQ

4glq


Resolution: 2.701→48.657 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 7 / Phase error: 23.79
RfactorNum. reflection% reflection
Rfree0.2378 397 4.7 %
Rwork0.1798 --
obs0.1824 8453 72.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 264.14 Å2 / Biso mean: 99.4901 Å2 / Biso min: 37.14 Å2
Refinement stepCycle: final / Resolution: 2.701→48.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 43 8 1554
Biso mean--76.14 62.86 -
Num. residues----183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091589
X-RAY DIFFRACTIONf_angle_d1.2562162
X-RAY DIFFRACTIONf_chiral_restr0.06239
X-RAY DIFFRACTIONf_plane_restr0.006273
X-RAY DIFFRACTIONf_dihedral_angle_d24.636938
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.701-2.79730.346280.316722320
2.7973-2.90920.2795110.332633931
2.9092-3.04160.4099290.28654150
3.0416-3.2020.3049330.292472666
3.202-3.40250.2922490.271990683
3.4025-3.66510.2755500.219198490
3.6651-4.03380.2293490.1906101792
4.0338-4.61710.2729510.1545105195
4.6171-5.81560.1912570.1389109796
5.8156-48.6570.1938600.1412117296
Refinement TLS params.Method: refined / Origin x: 20.5307 Å / Origin y: 45.9984 Å / Origin z: 19.8407 Å
111213212223313233
T0.638 Å20.239 Å20.034 Å2-0.7481 Å20.0118 Å2--0.3094 Å2
L11.4232 °2-5.6872 °20.8105 °2-6 °21.428 °2--4.3125 °2
S-0.844 Å °-1.0756 Å °-0.7012 Å °0.9149 Å °0.8681 Å °0.1523 Å °0.2612 Å °0.26 Å °0.0122 Å °
Refinement TLS groupSelection details: chain A

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