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- PDB-5mfc: Designed armadillo repeat protein YIIIM5AII in complex with (KR)4-GFP -

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Basic information

Entry
Database: PDB / ID: 5mfc
TitleDesigned armadillo repeat protein YIIIM5AII in complex with (KR)4-GFP
Components
  • (KR)4-Green fluorescent protein,Green fluorescent protein
  • YIIIM5AII
KeywordsDE NOVO PROTEIN / Designed armadillo repeat protein / peptide binding
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Alpha Horseshoe / Beta Barrel ...Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Alpha Horseshoe / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Green fluorescent protein
Similarity search - Component
Biological speciessynthetic construct (others)
Aequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHansen, S. / Kiefer, J. / Madhurantakam, C. / Mittl, P. / Plueckthun, A.
CitationJournal: Protein Sci. / Year: 2017
Title: Structures of designed armadillo repeat proteins binding to peptides fused to globular domains.
Authors: Hansen, S. / Kiefer, J.D. / Madhurantakam, C. / Mittl, P.R.E. / Pluckthun, A.
History
DepositionNov 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: (KR)4-Green fluorescent protein,Green fluorescent protein
C: YIIIM5AII
D: (KR)4-Green fluorescent protein,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,9395
Polymers117,8804
Non-polymers591
Water1,40578
1
A: YIIIM5AII
B: (KR)4-Green fluorescent protein,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9993
Polymers58,9402
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-1 kcal/mol
Surface area22200 Å2
MethodPISA
2
C: YIIIM5AII
D: (KR)4-Green fluorescent protein,Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)58,9402
Polymers58,9402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-1 kcal/mol
Surface area21310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.110, 124.240, 245.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein YIIIM5AII


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


Mass: 28912.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A059PIQ0
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 8% w/v PEG 4000, 0.1M Na acetate trihydrate pH 4.6,

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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 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→40.56 Å / Num. obs: 47804 / % possible obs: 97.9 % / Redundancy: 12.4 % / Biso Wilson estimate: 72.39 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 15.17
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 12.8 % / Rmerge(I) obs: 4.59 / Mean I/σ(I) obs: 0.58 / CC1/2: 0.174 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5aei, 1gfl

5aei

1gfl


Resolution: 2.4→40.56 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.386 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.368 / SU Rfree Blow DPI: 0.233 / SU Rfree Cruickshank DPI: 0.239
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2364 4.95 %RANDOM
Rwork0.218 ---
obs0.219 47802 97.9 %-
Displacement parametersBiso mean: 99.22 Å2
Baniso -1Baniso -2Baniso -3
1-10.0904 Å20 Å20 Å2
2--2.7678 Å20 Å2
3----12.8581 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: 1 / Resolution: 2.4→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7993 0 48 78 8119
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018257HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2511194HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2910SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes286HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1153HARMONIC5
X-RAY DIFFRACTIONt_it8211HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion22.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1072SEMIHARMONIC5
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_contact9339SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 167 4.8 %
Rwork0.193 3315 -
all0.195 3482 -
obs--98.16 %
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)
13.973-0.3741-1.27792.2645-0.86061.9668-0.09910.2349-0.9310.1393-0.13290.3455-0.0883-0.13190.232-0.36740.03550.0009-0.3328-0.2737-0.305218.811716.8561-42.7403
24.3598-0.70350.10032.5441-0.02651.10390.032-0.11250.05650.2301-0.1834-0.278-0.10490.14290.1514-0.0489-0.0561-0.0930.01290.0168-0.512950.878416.9911-43.5735
33.3179-0.49862.29933.35831.03884.217-0.2108-0.02550.23721.11770.09980.35740.31820.02870.1110.11390.09820.1786-0.4555-0.1476-0.57926.736.476-25.0242
42.5023-0.4341.66247.72530.6442.6617-0.47440.02950.30011.64080.2792-0.1113-0.19370.32320.19520.6860.0476-0.0178-0.2084-0.0877-0.764712.620364.9615-17.2901
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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