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- PDB-5mfj: Designed armadillo repeat protein YIII(Dq.V2)4CqI in complex with... -

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Basic information

Entry
Database: PDB / ID: 5mfj
TitleDesigned armadillo repeat protein YIII(Dq.V2)4CqI in complex with peptide (KR)5
Components
  • (KR)5
  • YIII(Dq.V2)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: 1.53 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 1.1Sep 20, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Feb 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 1.3May 8, 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

Downloads & links

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Assembly

Deposited unit
A: YIII(Dq.V2)4CqI
B: YIII(Dq.V2)4CqI
C: (KR)5
D: (KR)5


Theoretical massNumber of molelcules
Total (without water)54,4694
Polymers54,4694
Non-polymers00
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint15 kcal/mol
Surface area21580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.110, 89.250, 107.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein YIII(Dq.V2)4CqI


Mass: 25784.658 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: Protein/peptide (KR)5


Mass: 1449.883 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% PEG 2000 MME, 0.3M NaAcetate, 0.1M Tris, pH8.5

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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: Dec 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→46.13 Å / Num. obs: 74727 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 28.29 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.093 / Net I/σ(I): 16.98
Reflection shellResolution: 1.53→1.57 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.203 / Mean I/σ(I) obs: 0.56 / CC1/2: 0.104 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→46.13 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.095 / SU Rfree Blow DPI: 0.093 / SU Rfree Cruickshank DPI: 0.09
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3746 5.01 %RANDOM
Rwork0.206 ---
obs0.208 74702 100 %-
Displacement parametersBiso mean: 39.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.2019 Å20 Å20 Å2
2---1.4785 Å20 Å2
3---1.2766 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: 1 / Resolution: 1.53→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3746 0 0 476 4222
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094161HARMONIC2
X-RAY DIFFRACTIONt_angle_deg15698HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1561SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes175HARMONIC2
X-RAY DIFFRACTIONt_gen_planes592HARMONIC5
X-RAY DIFFRACTIONt_it4161HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.32
X-RAY DIFFRACTIONt_other_torsion19.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion556SEMIHARMONIC5
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_contact5527SEMIHARMONIC4
LS refinement shellResolution: 1.53→1.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 248 4.57 %
Rwork0.222 5183 -
all0.223 5431 -
obs--99.98 %
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)
10.68470.9253-0.53312.1695-1.06051.7124-0.0606-0.0128-0.159-0.118-0.1216-0.210.1050.12350.1822-0.01640.0270.0183-0.04450.0045-0.01992.6151.2746124.889
21.5879-0.72390.58230.5727-0.38671.0583-0.15450.070.12130.052-0.0332-0.0911-0.10130.05760.1877-0.0035-0.0167-0.0135-0.01750.0234-0.02219.4407-9.672494.1315
300.030.123600.217100.0086-0.03890.0279-0.04770.00970.03010.01960.0155-0.0183-0.01280.02940.00770.012-0.022-0.010512.45440.5188116.524
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ D|* }

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