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- PDB-5mfl: Designed armadillo repeat protein (KR)5_GS10_YIIIM6AII -

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Basic information

Entry
Database: PDB / ID: 5mfl
TitleDesigned armadillo repeat protein (KR)5_GS10_YIIIM6AII
Components(KR)5_GS10_YIIIM6AII
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: 2.5 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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.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.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: (KR)5_GS10_YIIIM6AII
B: (KR)5_GS10_YIIIM6AII
C: (KR)5_GS10_YIIIM6AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,65822
Polymers109,7223
Non-polymers93619
Water2,810156
1
A: (KR)5_GS10_YIIIM6AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9398
Polymers36,5741
Non-polymers3657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: (KR)5_GS10_YIIIM6AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8678
Polymers36,5741
Non-polymers2937
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: (KR)5_GS10_YIIIM6AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8526
Polymers36,5741
Non-polymers2785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.100, 93.100, 188.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-528-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein (KR)5_GS10_YIIIM6AII


Mass: 36573.855 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria)

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Non-polymers , 5 types, 175 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 37.5% (MPD/PEG1000/PEG3350), 0.03 M MgCl2, 0.03 M CaCl2, Bicine/TRIS pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→49.56 Å / Num. obs: 33299 / % possible obs: 99.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 66.91 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.165 / Net I/σ(I): 8.21
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 6.3 % / Rmerge(I) obs: 2.34 / Mean I/σ(I) obs: 0.61 / CC1/2: 0.127 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→49.56 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.896 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.93 / SU Rfree Blow DPI: 0.302 / SU Rfree Cruickshank DPI: 0.307
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1665 5 %RANDOM
Rwork0.206 ---
obs0.208 33299 99.5 %-
Displacement parametersBiso mean: 76.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.8156 Å20 Å20 Å2
2---1.8156 Å20 Å2
3---3.6313 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: 1 / Resolution: 2.5→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7441 0 42 156 7639
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087597HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1110321HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2718SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes300HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1042HARMONIC5
X-RAY DIFFRACTIONt_it7597HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.91
X-RAY DIFFRACTIONt_other_torsion20.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1018SEMIHARMONIC5
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_contact9423SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.252 142 5 %
Rwork0.238 2698 -
all0.238 2840 -
obs--99.86 %
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)
10.1852-0.11470.46261.0976-0.02573.5211-0.11010.01780.03070.0453-0.025-0.2476-0.70060.12770.13510.1718-0.0057-0.0734-0.0137-0.02610.0786-7.615456.1999-17.513
20.744-0.72250.34391.1001-0.85234.4667-0.11160.34460.0983-0.1154-0.173-0.2537-0.434-0.10340.28460.1155-0.02550.00520.13090.00980.1057-7.308250.5661-48.3976
30.9055-0.2908-0.4430.29650.2672.0180.01320.1182-0.2061-0.1457-0.12490.14390.1806-0.2420.11170.1140.0489-0.11620.0638-0.02570.1976-0.164110.0059-13.9475
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|11 - A|332 }
2X-RAY DIFFRACTION2{ B|11 - B|332 }
3X-RAY DIFFRACTION3{ C|12 - C|332 }

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