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- PDB-8q52: A PBP-like protein built from fragments of different folds -

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Basic information

Entry
Database: PDB / ID: 8q52
TitleA PBP-like protein built from fragments of different folds
ComponentsLeucine-specific-binding protein,Chemotaxis protein CheY
KeywordsDE NOVO PROTEIN / Protein fold evolution / gene duplication / flavodoxin-like fold / periplasmic-binding protein-like I fold / sub-domain / chimeric proteins / homology
Function / homology
Function and homology information


branched-chain amino acid transport / L-leucine binding / phenylalanine transport / archaeal or bacterial-type flagellum-dependent cell motility / L-leucine transport / phosphorelay signal transduction system / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / chemotaxis / outer membrane-bounded periplasmic space / membrane ...branched-chain amino acid transport / L-leucine binding / phenylalanine transport / archaeal or bacterial-type flagellum-dependent cell motility / L-leucine transport / phosphorelay signal transduction system / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / chemotaxis / outer membrane-bounded periplasmic space / membrane / metal ion binding / cytoplasm
Similarity search - Function
Leu/Ile/Val-binding protein / Leucine-binding protein domain / Periplasmic binding protein / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Periplasmic binding protein-like I
Similarity search - Domain/homology
Leucine-specific-binding protein / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Thermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsShanmugaratnam, S. / Toledo-Patino, S. / Goetz, S.K. / Farias-Rico, J.A. / Hocker, B.
Funding support Germany, European Union, Mexico, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)HO 4022/1-2 Germany
European Research Council (ERC)647548 'Protein Lego'European Union
Volkswagen Foundation94747 Germany
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)IA204622 Mexico
Consejo Nacional de Ciencia y Tecnologia (CONACYT)319320 Mexico
CitationJournal: Febs Lett. / Year: 2024
Title: Molecular handcraft of a well-folded protein chimera.
Authors: Toledo-Patino, S. / Goetz, S.K. / Shanmugaratnam, S. / Hocker, B. / Farias-Rico, J.A.
History
DepositionAug 8, 2023Deposition site: PDBE / Processing site: PDBE
SupersessionApr 10, 2024ID: 4QWV
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucine-specific-binding protein,Chemotaxis protein CheY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8434
Polymers34,5551
Non-polymers2883
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-26 kcal/mol
Surface area14080 Å2
Unit cell
Length a, b, c (Å)129.560, 129.560, 43.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-668-

HOH

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Components

#1: Protein Leucine-specific-binding protein,Chemotaxis protein CheY / L-BP / LS-BP


Mass: 34554.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Thermotoga maritima (bacteria)
Gene: livK, b3458, JW3423, cheY, TM_0700
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04816, UniProt: Q56312
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG 4000, 0.1M Tris.HCl, 0.3M Li sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2014
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→41.36 Å / Num. obs: 20824 / % possible obs: 99.85 % / Redundancy: 25.8 % / Biso Wilson estimate: 43.68 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.313 / Rpim(I) all: 0.06235 / Rrim(I) all: 0.3193 / Net I/σ(I): 14.41
Reflection shellResolution: 2.15→2.227 Å / Redundancy: 26.3 % / Rmerge(I) obs: 6.08 / Mean I/σ(I) obs: 0.62 / Num. unique obs: 2040 / CC1/2: 0.32 / CC star: 0.696 / Rpim(I) all: 1.197 / Rrim(I) all: 6.198 / % possible all: 98.92

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Processing

Software
NameVersionClassification
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
XDS20230630data reduction
XDS20230630data scaling
Coot0.9.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→41.36 Å / SU ML: 0.3455 / Cross valid method: FREE R-VALUE / Phase error: 28.6058
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 1041 5.01 %Random
Rwork0.2003 19756 --
obs0.2028 20797 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.81 Å2
Refinement stepCycle: LAST / Resolution: 2.15→41.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 15 168 2588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00162466
X-RAY DIFFRACTIONf_angle_d0.40833339
X-RAY DIFFRACTIONf_chiral_restr0.043378
X-RAY DIFFRACTIONf_plane_restr0.0031435
X-RAY DIFFRACTIONf_dihedral_angle_d3.6342341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.260.40371460.34762753X-RAY DIFFRACTION99.25
2.26-2.40.36911450.3142763X-RAY DIFFRACTION99.97
2.41-2.590.33521460.25732786X-RAY DIFFRACTION100
2.59-2.850.28071470.23082788X-RAY DIFFRACTION100
2.85-3.260.29761480.22242801X-RAY DIFFRACTION99.93
3.26-4.110.24711500.16872857X-RAY DIFFRACTION100
4.11-41.360.17781590.15853008X-RAY DIFFRACTION99.97

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