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- PDB-2ru4: Designed Armadillo Repeat Protein Self-ASsembled Complex (YIIM2-MAII) -

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Basic information

Entry
Database: PDB / ID: 2ru4
TitleDesigned Armadillo Repeat Protein Self-ASsembled Complex (YIIM2-MAII)
Components
  • Armadillo Repeat Protein, C-terminal fragment, MAII
  • Armadillo Repeat Protein, N-terminal fragment, YIIM2
KeywordsDE NOVO PROTEIN / solenoid repeat / Armadillo repeat motif / self-assembly / solution complex
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailsclosest to the average, model1
AuthorsZerbe, O. / Christen, M.T. / Plueckthun, A. / Watson, R.P.
CitationJournal: Structure / Year: 2014
Title: Spontaneous self-assembly of engineered armadillo repeat protein fragments into a folded structure
Authors: Watson, R.P. / Christen, M.T. / Ewald, C. / Bumbak, F. / Reichen, C. / Mihajlovic, M. / Schmidt, E. / Guntert, P. / Caflisch, A. / Pluckthun, A. / Zerbe, O.
History
DepositionNov 22, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Armadillo Repeat Protein, N-terminal fragment, YIIM2
B: Armadillo Repeat Protein, C-terminal fragment, MAII


Theoretical massNumber of molelcules
Total (without water)21,2982
Polymers21,2982
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Armadillo Repeat Protein, N-terminal fragment, YIIM2


Mass: 12193.524 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): M15
#2: Protein Armadillo Repeat Protein, C-terminal fragment, MAII


Mass: 9104.069 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): M15

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of the complex formed in solution by a split Armadillo repeat protein
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1313D HNCO
1413D HN(CA)CO
1513D HNCA
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D H(CCO)NH
1913D C(CO)NH
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY aliphatic
11312D 1H-15N HSQC
11412D 1H-13C HSQC aliphatic
11514D (H)CCH-TOCSY
11622D 1H-15N HSQC
11722D 1H-13C HSQC aliphatic
11823D 1H-15N NOESY
11923D 1H-13C NOESY aliphatic
12013D-13C edited/filtered NOESY
12123D-13C-edited/filtered NOESY
12223D-15N-edited/filtered NOESY
12323D CBCA(CO)NH
12423D HN(CA)CB
12523D HNCO
NMR detailsText: CHAINS A AND B ARE NOT COVALENTLY LINKED.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-13C; U-15N] YM2-1, 1.5 mM MA-2, 150 mM sodium phosphate-3, 150 mM sodium chloride-4, 2 % glycerol-5, 1 mM TMSP-6, 0.02 % sodium azide-7, 90% H2O/10% D2O90% H2O/10% D2O
20.75 mM [U-13C; U-15N] MA-8, 0.90 mM YM2-9, 150 mM sodium phosphate-10, 150 mM sodium chloride-11, 2 % glycerol-12, 1 mM TMSP-13, 0.02 % sodium azide-14, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMYM2-1[U-13C; U-15N]1
1.5 mMMA-21
150 mMsodium phosphate-31
150 mMsodium chloride-41
2 %glycerol-51
1 mMTMSP-61
0.02 %sodium azide-71
0.75 mMMA-8[U-13C; U-15N]2
0.90 mMYM2-92
150 mMsodium phosphate-102
150 mMsodium chloride-112
2 %glycerol-122
1 mMTMSP-132
0.02 %sodium azide-142
Sample conditionsIonic strength: 150 / pH: 7.4 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002
Varian DirectDriveVarianDirect Drive7003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CARA1.8.4Keller and Wuthrichchemical shift assignment
CcpNMR2.3.1CCPNpeak picking
CcpNMR2.3.1CCPNchemical shift assignment
CcpNMR2.3.1CCPNdata analysis
UNIO2.0.2(UNIO) Herrmanndata analysis
UNIO2.0.2(UNIO) Herrmannpeak picking
UNIO2.0.2(UNIO) Herrmannstructure solution
CYANA3.96aGuntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3.96aGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.32Schwieters, Kuszewski, Tjandra and Clorerefinement
TALOS-N4.01Shen and Baxdata analysis
CYANArefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: Structure calculation in vacuo, Refinement in explicit TIP3P water
NMR constraintsNOE constraints total: 1958 / NOE intraresidue total count: 531 / NOE long range total count: 404 / NOE medium range total count: 498 / NOE sequential total count: 525 / Protein phi angle constraints total count: 138 / Protein psi angle constraints total count: 141
NMR representativeSelection criteria: closest to the average
NMR ensembleAverage torsion angle constraint violation: 0.06 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 3.67 ° / Maximum upper distance constraint violation: 0.466 Å / Representative conformer: 1 / Torsion angle constraint violation method: PDBSTAT
NMR ensemble rmsDistance rms dev: 0.0323 Å / Distance rms dev error: 0.0011 Å

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