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- PDB-5mfk: Designed armadillo repeat protein YIII(Dq.V1)4CPAF in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5mfk
TitleDesigned armadillo repeat protein YIII(Dq.V1)4CPAF in complex with peptide (KR)4
Components
  • (KR)4
  • YIII(Dq.V1)4CPAF
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 / 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 1.2May 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.V1)4CPAF
B: YIII(Dq.V1)4CPAF
C: (KR)4
D: (KR)4


Theoretical massNumber of molelcules
Total (without water)54,0294
Polymers54,0294
Non-polymers00
Water2,846158
1
A: YIII(Dq.V1)4CPAF
C: (KR)4


Theoretical massNumber of molelcules
Total (without water)27,0152
Polymers27,0152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YIII(Dq.V1)4CPAF
D: (KR)4


Theoretical massNumber of molelcules
Total (without water)27,0152
Polymers27,0152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.470, 51.920, 69.680
Angle α, β, γ (deg.)90.00, 112.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein YIII(Dq.V1)4CPAF


Mass: 25851.041 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)4


Mass: 1163.510 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.: 158 / 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: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 2000 MME, 0.2 M KSCN, 0.1 M Na Acetate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40.41 Å / Num. obs: 20024 / % possible obs: 97.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 42.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.042 / Net I/σ(I): 21.8
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 5.36 / CC1/2: 0.923 / % possible all: 95.4

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.3→40.41 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.895 / SU R Cruickshank DPI: 0.406 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.41 / SU Rfree Blow DPI: 0.244 / SU Rfree Cruickshank DPI: 0.248
RfactorNum. reflection% reflectionSelection details
Rfree0.242 987 5 %RANDOM
Rwork0.184 ---
obs0.186 19733 98.5 %-
Displacement parametersBiso mean: 50.82 Å2
Baniso -1Baniso -2Baniso -3
1-8.4054 Å20 Å21.18 Å2
2---6.6786 Å20 Å2
3----1.7268 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 2.3→40.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3685 0 0 158 3843
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093749HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.135074HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1384SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes149HARMONIC2
X-RAY DIFFRACTIONt_gen_planes511HARMONIC5
X-RAY DIFFRACTIONt_it3749HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.3
X-RAY DIFFRACTIONt_other_torsion21.4
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion511SEMIHARMONIC5
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_contact4738SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.42 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.237 143 5 %
Rwork0.211 2715 -
all0.212 2858 -
obs--99.17 %
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)
12.5038-1.08710.08861.39260.00860.81570.0637-0.1823-0.2294-0.0826-0.0580.06380.15090.0688-0.0057-0.03910.037-0.0043-0.0091-0.0147-0.053122.93429.574711.911
21.7008-0.70751.31211.0995-1.34532.78030.04410.19860.2067-0.0837-0.07890.02350.00060.13370.0348-0.068-0.0090.0152-0.02390.0281-0.026640.963921.002533.018
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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