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- PDB-2lle: Computational design of an eight-stranded (beta/alpha)-barrel fro... -

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Basic information

Entry
Database: PDB / ID: 2lle
TitleComputational design of an eight-stranded (beta/alpha)-barrel from fragments of different folds
ComponentsChemotaxis protein CheY, Imidazole glycerol phosphate synthase subunit HisF chimera
KeywordsLYASE / (beta/alpha)8-barrel / TIM-barrel / Chimeric protein / Computationally designed protein
Function / homology
Function and homology information


imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / archaeal or bacterial-type flagellum-dependent cell motility / histidine biosynthetic process / phosphorelay signal transduction system / chemotaxis / lyase activity / metal ion binding / cytoplasm
Similarity search - Function
Histidine biosynthesis, HisF / Histidine biosynthesis protein / Histidine biosynthesis protein / Ribulose-phosphate binding barrel / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Aldolase class I ...Histidine biosynthesis, HisF / Histidine biosynthesis protein / Histidine biosynthesis protein / Ribulose-phosphate binding barrel / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chemotaxis protein CheY / Imidazole glycerol phosphate synthase subunit HisF
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model 1
Model type detailsminimized average
AuthorsColes, M. / Truffault, V. / Eisenbeis, S. / Proffitt, W. / Meiler, J. / Hocker, B.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Potential of fragment recombination for rational design of proteins.
Authors: Eisenbeis, S. / Proffitt, W. / Coles, M. / Truffault, V. / Shanmugaratnam, S. / Meiler, J. / Hocker, B.
History
DepositionNov 7, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chemotaxis protein CheY, Imidazole glycerol phosphate synthase subunit HisF chimera


Theoretical massNumber of molelcules
Total (without water)25,6081
Polymers25,6081
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 50structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein Chemotaxis protein CheY, Imidazole glycerol phosphate synthase subunit HisF chimera / / IGP synthase cyclase subunit / IGP synthase subunit HisF / ImGP synthase subunit HisF / IGPS subunit HisF


Mass: 25607.604 Da / Num. of mol.: 1 / Mutation: R4I, D78G, I95L, L201A,V213G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: cheY, TM_0700, hisF, TM_1036 / Production host: Escherichia coli (E. coli)
References: UniProt: Q56312, UniProt: Q9X0C6, Lyases; Carbon-carbon lyases; Oxo-acid-lyases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D HNCO
1223D HNCA
1323D HN(CA)CB
1423D C(CO)NH
1523D CCH-TOCSY
1623D CCH-COSY
1722D PLUSH-TACSY
1813D HNHA
1913D HNHB
11013D 1H-15N NOESY
11123D 1H-13C NOESY
11223D CNH-NOESY
11323D CCH-NOESY
11413D NNH-NOESY
11512D 15N-filtered 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 15N] CheYHisF-sfr_RM, 50 mM potassium phosphate, 300 mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] CheYHisF-sfr_RM, 50 mM potassium phosphate, 300 mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMCheYHisF-sfr_RM-1[U-100% 15N]1
50 mMpotassium phosphate-21
300 mMpotassium chloride-31
0.5 mMCheYHisF-sfr_RM-4[U-100% 13C; U-100% 15N]2
50 mMpotassium phosphate-52
300 mMpotassium chloride-62
Sample conditionsIonic strength: 350 / pH: 7.5 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceIIIBrukerAvanceIII6001
Bruker AvanceIIIBrukerAvanceIII8002

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Processing

NMR software
NameVersionDeveloperClassification
TOPSPINBruker Biospincollection
TOPSPINBruker Biospinprocessing
SPARKYGoddardchemical shift assignment
SPARKYGoddarddata analysis
X-PLOR_NIH2.21Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR_NIH2.21Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Non-bonded function including Ramachandran database potential
NMR constraintsProtein chi angle constraints total count: 128 / Protein other angle constraints total count: 44 / Protein phi angle constraints total count: 225 / Protein psi angle constraints total count: 224
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 17 / Maximum lower distance constraint violation: 0.04 Å / Maximum torsion angle constraint violation: 0.4 ° / Maximum upper distance constraint violation: 0.11 Å
NMR ensemble rmsDistance rms dev: 0.011 Å

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