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

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Basic information

Entry
Database: PDB / ID: 5mfh
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: 2 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)5
F: (RR)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,13127
Polymers123,2906
Non-polymers84221
Water9,584532
1
A: YIIIM5AII
E: (RR)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,93810
Polymers31,6172
Non-polymers3218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YIIIM5AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2286
Polymers30,0271
Non-polymers2005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: YIIIM5AII
F: (RR)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8989
Polymers31,6172
Non-polymers2817
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: YIIIM5AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0682
Polymers30,0271
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.480, 103.790, 134.010
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / 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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7 / Details: 5% PEG8000, 27.27% MPD, 0.1 M Na Cacodylate pH6.7

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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: 2→48.39 Å / Num. obs: 77426 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 35.55 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.543 / Net I/σ(I): 5.52
Reflection shellResolution: 2→2.05 Å / Redundancy: 11 % / Rmerge(I) obs: 9.23 / Mean I/σ(I) obs: 0.29 / CC1/2: 0.108 / % 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: 5MFE

5mfe


Resolution: 2→48.39 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.204 / SU Rfree Blow DPI: 0.165 / SU Rfree Cruickshank DPI: 0.165
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3721 5.02 %RANDOM
Rwork0.199 ---
obs0.2 74071 95.7 %-
Displacement parametersBiso mean: 44.57 Å2
Baniso -1Baniso -2Baniso -3
1--1.1342 Å20 Å20 Å2
2--2.7628 Å20 Å2
3----1.6287 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8536 0 21 532 9089
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088677HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0511810HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3094SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes357HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1195HARMONIC5
X-RAY DIFFRACTIONt_it8677HARMONIC20
X-RAY DIFFRACTIONt_nbd7SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.84
X-RAY DIFFRACTIONt_other_torsion18.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1162SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10776SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 144 4.95 %
Rwork0.206 2764 -
all0.207 2908 -
obs--51.76 %
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)
10.43380.06930.07370.5728-0.32980.7376-0.07080.117-0.0548-0.20740.10580.1430.1514-0.096-0.03510.1835-0.0304-0.02440.1747-0.02840.1647-15.9054-25.1014.684
20.23480.1655-0.13640.5393-0.56310.819-0.0133-0.0877-0.1160.055-0.0855-0.147-0.11760.07670.09890.11340.0225-0.05880.17240.07670.2546-10.4715-29.990534.5152
30.94270.3845-0.20260.9231-0.27521.4112-0.04110.06460.0875-0.1280.11670.0334-0.19780.0778-0.07560.0832-0.00830.03010.0691-0.04280.0502-8.102811.694624.5913
40.7501-0.1798-0.18441.5024-0.62421.4268-0.0344-0.048-0.01530.1982-0.05360.0226-0.0568-0.10020.0880.0373-0.0086-0.01150.0451-0.02480.093-33.63844.483840.702
50.8362-2.2236-1.04180.9786-0.54173.11580.21780.2560.05550.2530.1189-0.0404-0.8999-0.1916-0.33680.14020.0130.12970.3663-0.00070.2941-10.917413.280534.6613
60.5858-0.5951-0.4181.73450.41860.1657-0.17810.0133-0.0623-0.1730.15160.0259-0.0590.06440.02650.2658-0.01250.13250.3258-0.03790.1649-4.7263-32.37824.9485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|12 - A|293 }
2X-RAY DIFFRACTION2{ B|11 - B|292 }
3X-RAY DIFFRACTION3{ C|12 - C|292 }
4X-RAY DIFFRACTION4{ D|12 - D|293 }
5X-RAY DIFFRACTION5{ E|1 - E|8 }
6X-RAY DIFFRACTION6{ F|1 - F|8 }

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