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- PDB-6lnp: Crystal structure of citrate Biosensor -

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Basic information

Entry
Database: PDB / ID: 6lnp
TitleCrystal structure of citrate Biosensor
ComponentsFusion protein of Green fluorescent protein and Sensor histidine kinase CitA
KeywordsFLUORESCENT PROTEIN / Biosensor / Genetically Encoded / Citrate
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / bioluminescence / generation of precursor metabolites and energy / ATP binding / plasma membrane
Similarity search - Function
Single cache domain 3 / Single cache domain 3 / Signal transduction histidine kinase, sporulation regulator SpoOB / : / Periplasmic sensor-like domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Green Fluorescent Protein ...Single cache domain 3 / Single cache domain 3 / Signal transduction histidine kinase, sporulation regulator SpoOB / : / Periplasmic sensor-like domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Green Fluorescent Protein / Green fluorescent protein / Beta-Lactamase / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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 / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Green fluorescent protein / Sensor histidine kinase CitA
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Klebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.993 Å
AuthorsWen, Y. / Campbell, R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870132 China
Citation
Journal: Acs Cent.Sci. / Year: 2020
Title: High-Performance Intensiometric Direct- and Inverse-Response Genetically Encoded Biosensors for Citrate.
Authors: Zhao, Y. / Shen, Y. / Wen, Y. / Campbell, R.E.
#1: Journal: Biorxiv / Year: 2020
Title: High performance intensiometric direct- and inverse-response genetically encoded biosensors for citrate
Authors: Zhao, Y. / Shen, Y. / Wen, Y. / Campbell, R.
History
DepositionDec 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 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
B: Fusion protein of Green fluorescent protein and Sensor histidine kinase CitA
D: Fusion protein of Green fluorescent protein and Sensor histidine kinase CitA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1274
Polymers89,7432
Non-polymers3842
Water00
1
B: Fusion protein of Green fluorescent protein and Sensor histidine kinase CitA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0642
Polymers44,8721
Non-polymers1921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17530 Å2
MethodPISA
2
D: Fusion protein of Green fluorescent protein and Sensor histidine kinase CitA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0642
Polymers44,8721
Non-polymers1921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint3 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.410, 92.410, 123.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Fusion protein of Green fluorescent protein and Sensor histidine kinase CitA


Mass: 44871.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: citA / Production host: Escherichia coli (E. coli)
References: UniProt: P52687, UniProt: P42212*PLUS, histidine kinase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
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: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 4% Tacsimate pH 5.0, 12% Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.99→46.205 Å / Num. obs: 20881 / % possible obs: 99.76 % / Redundancy: 13.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.134 / Rrim(I) all: 0.143 / Net I/σ(I): 12.1
Reflection shellResolution: 2.99→3.1 Å / Num. unique obs: 2072 / CC1/2: 0.65

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GEL

6gel


Resolution: 2.993→46.205 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.99
RfactorNum. reflection% reflection
Rfree0.2823 1792 10.04 %
Rwork0.2227 --
obs0.2287 17843 85.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.84 Å2 / Biso mean: 51.3106 Å2 / Biso min: 18.69 Å2
Refinement stepCycle: final / Resolution: 2.993→46.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5552 0 26 0 5578
Biso mean--52.45 --
Num. residues----733
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.993-3.07350.438150.35741239
3.0735-3.16390.3196470.305143230
3.1639-3.2660.34661110.2997102972
3.266-3.38270.34511610.28521436100
3.3827-3.51810.33751630.27041442100
3.5181-3.67820.30961620.2541425100
3.6782-3.8720.28491660.23261433100
3.872-4.11440.27231610.21161453100
4.1144-4.43190.23751630.18271433100
4.4319-4.87750.26931640.18641460100
4.8775-5.58220.25241580.19871450100
5.5822-7.0290.30381600.23021452100
7.029-46.2050.24741610.19971483100
Refinement TLS params.Method: refined / Origin x: 18.3291 Å / Origin y: 21.4665 Å / Origin z: -13.3081 Å
111213212223313233
T0.2856 Å2-0.0732 Å2-0.113 Å2-0.3938 Å20.1469 Å2--0.3531 Å2
L0.37 °20.2506 °20.2487 °2-0.36 °20.2813 °2--0.9143 °2
S0.1943 Å °-0.1006 Å °-0.3088 Å °-0.0592 Å °0.0867 Å °0.1901 Å °0.2697 Å °-0.1818 Å °-0.18 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB-11 - 361
2X-RAY DIFFRACTION1allD-12 - 361
3X-RAY DIFFRACTION1allA1 - 2

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