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- PDB-4db6: Designed Armadillo repeat protein (YIIIM3AII) -

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Basic information

Entry
Database: PDB / ID: 4db6
TitleDesigned Armadillo repeat protein (YIIIM3AII)
ComponentsArmadillo repeat protein
KeywordsDE NOVO PROTEIN / Solenoid repeat / Armadillo repeat motif
Function / homologyLeucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMadhurantakam, C. / Varadamsetty, G. / Grutter, M.G. / Pluckthun, A. / Mittl, P.R.E.
CitationJournal: Protein Sci. / Year: 2012
Title: Structure-based optimization of designed Armadillo-repeat proteins.
Authors: Madhurantakam, C. / Varadamsetty, G. / Grutter, M.G. / Pluckthun, A. / Mittl, P.R.
History
DepositionJan 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Database references
Revision 1.2Sep 5, 2012Group: Structure summary
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Armadillo repeat protein


Theoretical massNumber of molelcules
Total (without water)22,4831
Polymers22,4831
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.960, 91.580, 92.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

21A-425-

HOH

31A-440-

HOH

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Components

#1: Protein Armadillo repeat protein


Mass: 22482.998 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): XL1 Blue
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES,pH 7.5, 1.4 M sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.93 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 1, 2010 / Details: Mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.57→30 Å / Num. obs: 26356 / % possible obs: 98.7 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 15.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→22.895 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 20.34 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2231 862 5.04 %random
Rwork0.1815 ---
obs0.1837 25608 98.46 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.783 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 30.5164 Å2
Baniso -1Baniso -2Baniso -3
1--2.617 Å20 Å2-0 Å2
2--5.9268 Å2-0 Å2
3----3.3098 Å2
Refinement stepCycle: LAST / Resolution: 1.8→22.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 0 153 1615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061587
X-RAY DIFFRACTIONf_angle_d0.9512181
X-RAY DIFFRACTIONf_dihedral_angle_d15.761601
X-RAY DIFFRACTIONf_chiral_restr0.064251
X-RAY DIFFRACTIONf_plane_restr0.005298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.91280.24911490.19692611X-RAY DIFFRACTION97
1.9128-2.06040.24711470.17852665X-RAY DIFFRACTION99
2.0604-2.26750.20211260.16252706X-RAY DIFFRACTION99
2.2675-2.59530.20591440.17032728X-RAY DIFFRACTION100
2.5953-3.26820.24831480.18582772X-RAY DIFFRACTION100
3.2682-22.89680.21391480.18692770X-RAY DIFFRACTION96

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