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- PDB-8zex: Biosensor HaloKbp1a -

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Basic information

Entry
Database: PDB / ID: 8zex
TitleBiosensor HaloKbp1a
ComponentsHaloKbp1a
KeywordsFLUORESCENT PROTEIN / Genetically Encoded Biosensor / Potassium Binding Protein / HaloTag
Function / homology:
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsWen, Y. / Campbell, R.E.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: High-Performance Chemigenetic Potassium Ion Indicator.
Authors: Cheng, D. / Ouyang, Z. / He, X. / Nasu, Y. / Wen, Y. / Terai, T. / Campbell, R.E.
History
DepositionMay 7, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HaloKbp1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9082
Polymers53,8691
Non-polymers391
Water6,738374
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.590, 50.280, 58.830
Angle α, β, γ (deg.)94.00, 101.32, 99.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein HaloKbp1a


Mass: 53868.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M PCTP, pH 6.0 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.66→18.24 Å / Num. obs: 55656 / % possible obs: 95.93 % / Redundancy: 3.5 % / CC1/2: 0.997 / Net I/σ(I): 9.4
Reflection shellResolution: 1.66→1.72 Å / Num. unique obs: 5509 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→18.24 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2041 1999 3.6 %
Rwork0.1832 --
obs0.184 55604 96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.66→18.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3432 0 1 374 3807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083544
X-RAY DIFFRACTIONf_angle_d1.0434841
X-RAY DIFFRACTIONf_dihedral_angle_d5.523469
X-RAY DIFFRACTIONf_chiral_restr0.064531
X-RAY DIFFRACTIONf_plane_restr0.009631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.70.34571410.3253769X-RAY DIFFRACTION95
1.7-1.750.351410.29113801X-RAY DIFFRACTION95
1.75-1.80.27341430.2653828X-RAY DIFFRACTION96
1.8-1.860.28311430.24173826X-RAY DIFFRACTION95
1.86-1.920.27341420.21963791X-RAY DIFFRACTION96
1.92-20.23661420.20323835X-RAY DIFFRACTION96
2-2.090.18941420.19083840X-RAY DIFFRACTION96
2.09-2.20.23231440.18463836X-RAY DIFFRACTION96
2.2-2.340.22861430.18533821X-RAY DIFFRACTION96
2.34-2.520.23481430.19033845X-RAY DIFFRACTION96
2.52-2.770.25031440.19833866X-RAY DIFFRACTION96
2.77-3.170.20981430.18343815X-RAY DIFFRACTION96
3.17-3.990.15721430.15963817X-RAY DIFFRACTION96
3.99-18.240.14491450.14543915X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -6.7273 Å / Origin y: 7.0544 Å / Origin z: -9.25 Å
111213212223313233
T0.1651 Å2-0.0044 Å20.0134 Å2-0.1795 Å2-0.0166 Å2--0.1803 Å2
L0.4197 °2-0.0873 °20.1423 °2-1.0955 °2-0.129 °2--0.3953 °2
S-0.0132 Å °-0.0078 Å °-0.0257 Å °-0.0913 Å °0.0028 Å °0.0289 Å °-0.0394 Å °-0.0223 Å °0.0058 Å °
Refinement TLS groupSelection details: all

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