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

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Basic information

Entry
Database: PDB / ID: 5mfi
TitleDesigned armadillo repeat protein YIII(Dq.V2)4CqI in complex with peptide (KR)4
Components
  • (KR)4
  • YIII(Dq.V2)4CqI
KeywordsDE NOVO PROTEIN / Designed armadillo repeat protein / peptide binding / de novo proein
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: 1.45 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.V2)4CqI
B: YIII(Dq.V2)4CqI
C: (KR)4
D: (KR)4


Theoretical massNumber of molelcules
Total (without water)53,8964
Polymers53,8964
Non-polymers00
Water10,449580
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint11 kcal/mol
Surface area21240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.800, 89.250, 107.500
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)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.: 580 / 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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 2000 MME, 0.3 M Na Acetate, 0.1M Na Acetate, pH5.5

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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: 1.45→46.04 Å / Num. obs: 87337 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 24.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Net I/σ(I): 15.1
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 12.5 % / Rmerge(I) obs: 5.435 / Mean I/σ(I) obs: 0.52 / CC1/2: 0.12 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→46.04 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.083 / SU Rfree Blow DPI: 0.081 / SU Rfree Cruickshank DPI: 0.077
RfactorNum. reflection% reflectionSelection details
Rfree0.228 4375 5.01 %RANDOM
Rwork0.202 ---
obs0.203 87276 100 %-
Displacement parametersBiso mean: 34.92 Å2
Baniso -1Baniso -2Baniso -3
1--1.4091 Å20 Å20 Å2
2---0.387 Å20 Å2
3---1.7961 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 1.45→46.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3726 0 0 580 4306
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094221HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.045779HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1604SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes182HARMONIC2
X-RAY DIFFRACTIONt_gen_planes603HARMONIC5
X-RAY DIFFRACTIONt_it4221HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.36
X-RAY DIFFRACTIONt_other_torsion19.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion563SEMIHARMONIC5
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_contact5796SEMIHARMONIC4
LS refinement shellResolution: 1.45→1.49 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 298 4.67 %
Rwork0.236 6086 -
all0.236 6384 -
obs--99.94 %
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)
10.40430.6544-0.27372.0003-0.86671.3208-0.0713-0.0066-0.101-0.1526-0.0886-0.19040.07260.08370.1599-0.03380.02210.0259-0.02050.0037-0.02942.68841.2059124.976
21.9784-0.81230.71990.6035-0.4450.7498-0.13670.07070.08010.0452-0.0273-0.0974-0.09780.04260.1641-0.0143-0.0132-0.00680.00820.0188-0.02729.512-9.810594.8255
30.47780.6279-0.86360-0.152100.0040.0216-0.03770.0010.0144-0.07920.01620.0163-0.01840.0017-0.00590.0360.02720.0066-0.038410.85121.6588133.128
400.44060.01860-0.34050.0020.0003-0.01810.06490.01760.0153-0.02120.00040.0106-0.01550.02320.0335-0.0187-0.0093-0.0136-0.02612.4018-2.2784109.256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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