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- PDB-5mfm: Designed armadillo repeat protein peptide fusion YIIIM6AII_GS11_(KR)5 -

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Basic information

Entry
Database: PDB / ID: 5mfm
TitleDesigned armadillo repeat protein peptide fusion YIIIM6AII_GS11_(KR)5
Components
  • Importin subunit alpha
  • YIIIM6AII_GS11_(KR)5
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)
Candida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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_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.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: YIIIM6AII_GS11_(KR)5
B: YIIIM6AII_GS11_(KR)5
C: Importin subunit alpha
D: YIIIM6AII_GS11_(KR)5
E: YIIIM6AII_GS11_(KR)5
F: YIIIM6AII_GS11_(KR)5
P: YIIIM6AII_GS11_(KR)5
Q: YIIIM6AII_GS11_(KR)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,07047
Polymers291,5338
Non-polymers1,53739
Water6,449358
1
A: YIIIM6AII_GS11_(KR)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7179
Polymers36,4061
Non-polymers3118
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YIIIM6AII_GS11_(KR)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6157
Polymers36,4061
Non-polymers2096
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Importin subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,02110
Polymers36,6921
Non-polymers3299
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: YIIIM6AII_GS11_(KR)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,77310
Polymers36,4061
Non-polymers3679
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: YIIIM6AII_GS11_(KR)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4543
Polymers36,4061
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: YIIIM6AII_GS11_(KR)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6786
Polymers36,4061
Non-polymers2735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
P: YIIIM6AII_GS11_(KR)5


Theoretical massNumber of molelcules
Total (without water)36,4061
Polymers36,4061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
Q: YIIIM6AII_GS11_(KR)5


Theoretical massNumber of molelcules
Total (without water)36,4061
Polymers36,4061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.760, 89.390, 123.850
Angle α, β, γ (deg.)90.00, 97.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ABDEFPQC

#1: Protein
YIIIM6AII_GS11_(KR)5


Mass: 36405.797 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria)
#2: Protein Importin subunit alpha


Mass: 36692.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Gene: AO440_003254, AO440_005522 / Production host: Escherichia coli K-12 (bacteria)

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Non-polymers , 4 types, 397 molecules

#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.02 Å3/Da / Density % sol: 38.96 %
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: X06DA / 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: 2.3→44.69 Å / Num. obs: 77719 / % possible obs: 98.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 50.87 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Net I/σ(I): 8.67
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.63 / Mean I/σ(I) obs: 1.07 / CC1/2: 0.156 / % possible all: 99.1

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→44.69 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.59 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.533 / SU Rfree Blow DPI: 0.258 / SU Rfree Cruickshank DPI: 0.267
RfactorNum. reflection% reflectionSelection details
Rfree0.251 3887 5 %RANDOM
Rwork0.217 ---
obs0.219 77719 98.6 %-
Displacement parametersBiso mean: 78.71 Å2
Baniso -1Baniso -2Baniso -3
1-2.8082 Å20 Å23.3082 Å2
2---3.5701 Å20 Å2
3---0.7619 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: 1 / Resolution: 2.3→44.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15537 0 57 358 15952
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00816218HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0321933HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5933SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes636HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2227HARMONIC5
X-RAY DIFFRACTIONt_it16218HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.64
X-RAY DIFFRACTIONt_other_torsion21.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2146SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies52HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact19869SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 286 5 %
Rwork0.258 5436 -
all0.259 5722 -
obs--98.9 %
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)
11.8286-0.4351.480.79550.69942.4966-0.1289-0.10180.11770.0989-0.00010.11980.0837-0.12940.129-0.1091-0.01560.003-0.0551-0.0335-0.0282-1.99611.9414-25.6833
22.5282-0.03031.44690.9245-0.30461.68420.02040.2430.0827-0.13040.02140.22570.3371-0.1097-0.0418-0.1098-0.0335-0.1097-0.03210.065-0.0662-16.451947.221411.5232
30.3970.1706-0.01980-0.0043-0.0110.00090.0029-0.00250.0010.00540.0057-0.0089-0.0031-0.0063-0.02160.0008-0.00910.0044-0.0168-0.0054-93.034844.4305-41.1398
43.18420.07831.18181.003-0.58511.06730.0932-0.3978-0.0203-0.2141-0.1238-0.1780.2231-0.13990.0307-0.07340.02250.0157-0.03680.0331-0.0947-57.357.4835-56.365
5-0.0389-0.35950.14560-0.27390.3663-0.002-0.0013-0.0017-0.00750.00080.0052-0.0064-0.00380.00120.00920.0036-0.0465-0.01740.0232-0.024-69.340919.3334-88.8374
66.01670.02283.37360.6911-0.02772.30990.1189-0.32750.24160.0475-0.3032-0.05880.23310.00820.1843-0.134-0.0522-0.0060.00860.0082-0.2621-43.396644.2471-16.4024
74.02010.79450.97270-0.36162.53440.1164-0.54960.166-0.0706-0.2137-0.04690.02690.06310.0973-0.18660.0194-0.00250.0125-0.0612-0.1214-35.185513.7472-46.1899
83.63990.6482.48260.8389-0.39162.81950.01350.22960.3481-0.0115-0.28020.09720.24720.31770.2667-0.10020.01250.0134-0.04580.003-0.1367-56.678649.9758-37.2937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ P|* }
4X-RAY DIFFRACTION4{ C|* }
5X-RAY DIFFRACTION5{ Q|* }
6X-RAY DIFFRACTION6{ D|* }
7X-RAY DIFFRACTION7{ E|* }
8X-RAY DIFFRACTION8{ F|* }

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