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Basic information

Entry
Database: PDB / ID: 9ws1
TitleToFrO 15E_cryo
Componentshistidine kinase
KeywordsFLUORESCENT PROTEIN / cyanobacteria / cyanobacteriochrome / pcb / photoreceptor / water molecules
Function / homologyPHYCOCYANOBILIN / :
Function and homology information
Biological speciesTolypothrix sp. PCC 7910 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKim, Y. / Yang, H.W. / Liu, X. / Liu, H. / Park, Y.I. / Yun, J.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2025-25427247 Korea, Republic Of
Other governmentIBS-R021-D1-2023-a00 Korea, Republic Of
CitationJournal: To Be Published
Title: ToFrO 15E_cryo
Authors: Kim, Y. / Yang, H.W. / Liu, X. / Liu, H. / Park, Y.I. / Yun, J.H.
History
DepositionSep 12, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,7584
Polymers41,5812
Non-polymers1,1772
Water4,576254
1
B: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3792
Polymers20,7901
Non-polymers5891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3792
Polymers20,7901
Non-polymers5891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.040, 53.870, 79.950
Angle α, β, γ (deg.)90.000, 101.150, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein histidine kinase


Mass: 20790.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tolypothrix sp. PCC 7910 (bacteria) / Gene: HCG51_32595 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6G9SQI3, histidine kinase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 5% (w/v) 1-Ethyl-3-methylimidazolium trifluoromethanesulfonate, 15% (w/v) PEG 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→28.61 Å / Num. obs: 36676 / % possible obs: 96.1 % / Redundancy: 6.1 % / Biso Wilson estimate: 12.14 Å2 / CC1/2: 0.98 / Net I/σ(I): 7.74
Reflection shellResolution: 1.8→1.88 Å / Num. unique obs: 3653 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UV8

6uv8


Resolution: 1.8→27.87 Å / SU ML: 0.2149 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.9733
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2422 1834 5 %
Rwork0.2195 34821 -
obs0.2206 36655 96.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.43 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 86 254 2740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692535
X-RAY DIFFRACTIONf_angle_d1.01613464
X-RAY DIFFRACTIONf_chiral_restr0.0576400
X-RAY DIFFRACTIONf_plane_restr0.0059434
X-RAY DIFFRACTIONf_dihedral_angle_d15.0356884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.33181380.26282618X-RAY DIFFRACTION95.56
1.85-1.90.28241450.23692771X-RAY DIFFRACTION99.56
1.9-1.960.3311450.26292754X-RAY DIFFRACTION98.64
1.96-2.030.24311440.22172722X-RAY DIFFRACTION98.86
2.03-2.120.25931420.21612705X-RAY DIFFRACTION98.31
2.12-2.210.27021360.212579X-RAY DIFFRACTION92.69
2.21-2.330.28941440.26272739X-RAY DIFFRACTION98.73
2.33-2.470.24831440.2122744X-RAY DIFFRACTION98.7
2.47-2.670.21821440.21062724X-RAY DIFFRACTION98.02
2.67-2.930.24851300.222471X-RAY DIFFRACTION88.71
2.93-3.360.23231450.21262748X-RAY DIFFRACTION98.1
3.36-4.230.19891370.20542609X-RAY DIFFRACTION92.71
4.23-27.870.19021400.19362637X-RAY DIFFRACTION91.71
Refinement TLS params.Method: refined / Origin x: 14.5036885084 Å / Origin y: -11.3969190904 Å / Origin z: 10.932774943 Å
111213212223313233
T0.0480045740197 Å20.00891265184638 Å20.0261114537178 Å2-0.0555159206993 Å20.0220595732317 Å2--0.0979724530428 Å2
L0.448767291776 °20.209832291363 °20.218798828114 °2-0.871802630175 °20.666224176658 °2--1.14171293406 °2
S-0.00291127345082 Å °-0.0299185488808 Å °0.00502439331474 Å °0.0866379981518 Å °0.00077972256983 Å °0.0781242402053 Å °0.0346808929242 Å °-0.00522415260224 Å °-0.0094374815978 Å °
Refinement TLS groupSelection details: all

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