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- PDB-5mff: Designed armadillo repeat protein YIIIM5AII in complex with pepti... -

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Basic information

Entry
Database: PDB / ID: 5mff
TitleDesigned armadillo repeat protein YIIIM5AII in complex with peptide (RR)5
Components
  • (RR)5
  • YIIIM5AII
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: 1.9 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: YIIIM5AII
B: YIIIM5AII
C: YIIIM5AII
D: YIIIM5AII
E: (RR)5
F: (RR)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,15920
Polymers123,2906
Non-polymers86914
Water7,134396
1
A: YIIIM5AII
B: YIIIM5AII
E: (RR)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0179
Polymers61,6453
Non-polymers3726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: YIIIM5AII
D: YIIIM5AII
F: (RR)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,14111
Polymers61,6453
Non-polymers4978
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.755, 90.886, 179.659
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
YIIIM5AII


Mass: 30027.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria)
#2: Protein/peptide (RR)5


Mass: 1589.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 60% (NH4)2 SO4, 0.1M HEPES pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.31 Å / Num. obs: 106118 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 44.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Net I/σ(I): 14.51
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 11.2 % / Rmerge(I) obs: 4.68 / Mean I/σ(I) obs: 0.7 / CC1/2: 0.27 / % 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: 1.9→48.31 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.126 / SU Rfree Blow DPI: 0.118 / SU Rfree Cruickshank DPI: 0.119
RfactorNum. reflection% reflectionSelection details
Rfree0.213 5293 5 %RANDOM
Rwork0.184 ---
obs0.186 105947 99.9 %-
Displacement parametersBiso mean: 52.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.7857 Å20 Å20 Å2
2---1.7785 Å20 Å2
3---0.9929 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: 1 / Resolution: 1.9→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8502 0 56 396 8954
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018789HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1111953HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3151SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes356HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1218HARMONIC5
X-RAY DIFFRACTIONt_it8789HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.47
X-RAY DIFFRACTIONt_other_torsion19.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1173SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies18HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10889SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 374 4.87 %
Rwork0.24 7309 -
all0.24 7683 -
obs--99.23 %
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)
11.07730.9823-0.23821.7833-0.53730.632-0.0253-0.03530.0376-0.07820.050.04680.1286-0.0951-0.0247-0.3203-0.0639-0.0062-0.29370.0046-0.330930.60076.4727192.951
20.33340.0854-0.51850.16260.1230.95860.0603-0.01750.13630.1643-0.1623-0.02380.1703-0.00670.1020.3208-0.1206-0.04070.1415-0.20120.1136-9.284615.4607233.348
32.86060.78630.93691.1320.09461.0480.1682-0.128-0.16040.0602-0.0947-0.12020.1645-0.1277-0.0735-0.3157-0.0629-0.0145-0.33420.0163-0.3889-17.097516.7311215.694
40.2756-0.054-0.55190.31140.43081.1914-0.0064-0.0690.0597-0.15250.1598-0.2075-0.37160.1634-0.15350.1796-0.1220.07220.1834-0.01610.343830.41289.1441173.764
50.31440.68080.35780.0299-0.48252.3812-0.07430.0570.0756-0.0751-0.0398-0.0660.2602-0.04460.1141-0.11450.00130.01490.09150.1357-0.158229.28314.6981182.244
60-0.9198-0.74620.00520.60232.30950.0196-0.02960.06930.0085-0.228-0.1790.086-0.1390.20830.092-0.0033-0.1206-0.02960.0334-0.2161-16.336416.7862225.509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

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