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- PDB-5mfb: Designed armadillo repeat protein YIII(Dq)4CqI -

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Basic information

Entry
Database: PDB / ID: 5mfb
TitleDesigned armadillo repeat protein YIII(Dq)4CqI
ComponentsYIII(Dq)4CqI
KeywordsDE NOVO PROTEIN / Designed armadillo repeat protein / peptide binding
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: 2.3 Å
AuthorsHansen, S. / Ernst, P. / Reichen, C. / Ewald, C. / Mittl, P. / Plueckthun, A.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Curvature of designed armadillo repeat proteins allows modular peptide binding.
Authors: Hansen, S. / Ernst, P. / Konig, S.L.B. / Reichen, C. / Ewald, C. / Nettels, D. / Mittl, P.R.E. / Schuler, B. / Pluckthun, A.
History
DepositionNov 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0May 8, 2024Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YIII(Dq)4CqI
B: YIII(Dq)4CqI


Theoretical massNumber of molelcules
Total (without water)50,4092
Polymers50,4092
Non-polymers00
Water1,24369
1
A: YIII(Dq)4CqI


Theoretical massNumber of molelcules
Total (without water)25,2041
Polymers25,2041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YIII(Dq)4CqI


Theoretical massNumber of molelcules
Total (without water)25,2041
Polymers25,2041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.230, 46.560, 90.810
Angle α, β, γ (deg.)90.00, 128.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-307-

HOH

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Components

#1: Protein YIII(Dq)4CqI


Mass: 25204.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.3 M Na-Acetate, 0.1 M Na-Cacodylate pH 6.5, 25 % PEG 2K MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→42.81 Å / Num. obs: 20111 / % possible obs: 97.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 57.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Net I/σ(I): 10.31
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4 % / Rmerge(I) obs: 1.85 / Mean I/σ(I) obs: 0.76 / CC1/2: 0.298 / % possible all: 97.1

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→42.81 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.331 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.319 / SU Rfree Blow DPI: 0.229 / SU Rfree Cruickshank DPI: 0.235
RfactorNum. reflection% reflectionSelection details
Rfree0.241 975 4.85 %RANDOM
Rwork0.184 ---
obs0.187 20111 97.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8611 Å20 Å26.5212 Å2
2---4.7727 Å20 Å2
3---2.9117 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.3→42.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 0 69 3555
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013500HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.294746HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1280SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes152HARMONIC2
X-RAY DIFFRACTIONt_gen_planes477HARMONIC5
X-RAY DIFFRACTIONt_it3500HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.4
X-RAY DIFFRACTIONt_other_torsion21.55
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion498SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4244SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.42 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.249 133 4.6 %
Rwork0.228 2761 -
all0.229 2894 -
obs--97.27 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8591-1.5817-1.3981.8888-0.04913.9954-0.3698-0.22520.20130.0313-0.0416-0.0203-0.22020.32450.4115-0.12090.0687-0.0798-0.2072-0.0616-0.2793-52.797212.070283.5144
22.38010.221-0.29273.7681-1.91484.49480.32970.2647-0.43590.3532-0.4031-0.52460.175-0.20590.0735-0.2655-0.047-0.0356-0.17130.0583-0.1895-28.741630.464198.3572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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