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- PDB-5mfe: Designed armadillo repeat protein YIIIM5AII in complex with (RR)4... -

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Basic information

Entry
Database: PDB / ID: 5mfe
TitleDesigned armadillo repeat protein YIIIM5AII in complex with (RR)4 peptide
Components
  • (RR)4
  • 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: 1.95 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 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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)4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,97637
Polymers121,3855
Non-polymers1,59032
Water8,251458
1
B: YIIIM5AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2545
Polymers30,0271
Non-polymers2264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: YIIIM5AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,51212
Polymers30,0271
Non-polymers48511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: YIIIM5AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3787
Polymers30,0271
Non-polymers3506
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: YIIIM5AII
E: (RR)4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,83213
Polymers31,3032
Non-polymers52911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-21 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.000, 103.673, 134.182
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)4


Mass: 1275.566 Da / Num. of mol.: 1 / 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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: PEG8000 5%, MPD 27.27%, NaCacodylate 0.1M pH7 200mM CaCl2

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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: 1.95→48.35 Å / Num. obs: 83955 / % possible obs: 99.9 % / Redundancy: 8.6 % / Biso Wilson estimate: 33.38 Å2 / Rmerge(I) obs: 0.241 / Net I/σ(I): 7.94
Reflection shellResolution: 1.95→2 Å / Redundancy: 8.8 % / Rmerge(I) obs: 3.68 / Mean I/σ(I) obs: 0.6 / CC1/2: 0.155 / % 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
Starting model: 5MFC

5mfc


Resolution: 1.95→48.35 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.156 / SU Rfree Blow DPI: 0.147 / SU Rfree Cruickshank DPI: 0.148
RfactorNum. reflection% reflectionSelection details
Rfree0.23 4163 5 %RANDOM
Rwork0.181 ---
obs0.183 83318 99.3 %-
Displacement parametersBiso mean: 40.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.7323 Å20 Å20 Å2
2--2.7384 Å20 Å2
3----1.0061 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 1.95→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8433 0 74 458 8965
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018675HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1311799HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3069SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes357HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1188HARMONIC5
X-RAY DIFFRACTIONt_it8675HARMONIC20
X-RAY DIFFRACTIONt_nbd7SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.38
X-RAY DIFFRACTIONt_other_torsion18.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1157SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies8HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11145SEMIHARMONIC4
LS refinement shellResolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 284 5.02 %
Rwork0.226 5378 -
all0.227 5662 -
obs--92.18 %
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)
10.75560.4753-0.27020.8158-0.32131.42670.01040.04630.0935-0.07130.13740.0604-0.30430.0921-0.1477-0.01790.00110.0344-0.0719-0.0434-0.0823-8.161611.695224.8312
21.025-0.3055-0.01331.6503-0.68041.5306-0.0262-0.06170.08240.1767-0.05140.0102-0.0994-0.14850.0777-0.0895-0.0178-0.0264-0.1199-0.032-0.0648-33.57424.550940.9382
30.09840.2054-0.16590.7009-0.62140.9492-0.00940.0601-0.0694-0.1560.0459-0.01250.0696-0.0694-0.0366-0.01020.0114-0.022-0.04370.0305-0.0024-15.8618-25.11684.7921
40.73630.25660.01390.8581-0.46730.9927-0.037-0.111-0.09430.03210.01780.0180.0352-0.03540.0191-0.05020.04680.0153-0.03730.0139-0.0563-10.4715-30.056634.3101
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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