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- PDB-4dba: Designed Armadillo repeat protein (YIIM3AII) -

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Basic information

Entry
Database: PDB / ID: 4dba
TitleDesigned Armadillo repeat protein (YIIM3AII)
ComponentsDesigned Armadillo repeat protein, YIIM3AII
KeywordsDE NOVO PROTEIN / Solenoid repeat / Armadillo repeat motif
Function / homologyLeucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMadhurantakam, C. / Varadamsetty, G. / Grutter, M.G. / Pluckthun, A. / Mittl, P.R.E.
CitationJournal: Protein Sci. / Year: 2012
Title: Structure-based optimization of designed Armadillo-repeat proteins.
Authors: Madhurantakam, C. / Varadamsetty, G. / Grutter, M.G. / Pluckthun, A. / Mittl, P.R.
History
DepositionJan 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Database references
Revision 1.2Sep 5, 2012Group: Structure summary
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Designed Armadillo repeat protein, YIIM3AII
B: Designed Armadillo repeat protein, YIIM3AII
C: Designed Armadillo repeat protein, YIIM3AII
D: Designed Armadillo repeat protein, YIIM3AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9739
Polymers90,5124
Non-polymers4605
Water1,26170
1
A: Designed Armadillo repeat protein, YIIM3AII
B: Designed Armadillo repeat protein, YIIM3AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5325
Polymers45,2562
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-29 kcal/mol
Surface area17530 Å2
MethodPISA
2
C: Designed Armadillo repeat protein, YIIM3AII
D: Designed Armadillo repeat protein, YIIM3AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4404
Polymers45,2562
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-29 kcal/mol
Surface area17560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.151, 60.603, 61.862
Angle α, β, γ (deg.)74.82, 89.55, 75.53
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Designed Armadillo repeat protein, YIIM3AII


Mass: 22628.092 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.05 M succinic acid, pH 4.0, 20% PEG 4000, 0.2 M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 11, 2010 / Details: Helios optical system
RadiationMonochromator: Helios multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→36.56 Å / Num. obs: 26658 / % possible obs: 92.8 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 57.5 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 2.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→25.288 Å / SU ML: 0.47 / σ(F): 0 / Phase error: 37.56 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3014 1353 5.08 %random
Rwork0.2336 ---
obs0.237 26658 89.65 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.335 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6767 Å2-1.1135 Å2-3.136 Å2
2---6.3638 Å2-8.8511 Å2
3---10.0405 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5876 0 30 70 5976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095952
X-RAY DIFFRACTIONf_angle_d1.2038074
X-RAY DIFFRACTIONf_dihedral_angle_d18.9862227
X-RAY DIFFRACTIONf_chiral_restr0.073953
X-RAY DIFFRACTIONf_plane_restr0.0051089
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.48580.4341240.35332355X-RAY DIFFRACTION83
2.4858-2.58520.41791240.34252409X-RAY DIFFRACTION86
2.5852-2.70270.41971290.33532424X-RAY DIFFRACTION85
2.7027-2.8450.42391280.32112407X-RAY DIFFRACTION86
2.845-3.0230.39281180.29692441X-RAY DIFFRACTION86
3.023-3.2560.35511560.2812584X-RAY DIFFRACTION91
3.256-3.58280.33771410.27712642X-RAY DIFFRACTION94
3.5828-4.09940.31171280.21882661X-RAY DIFFRACTION94
4.0994-5.15760.29291580.19662674X-RAY DIFFRACTION95
5.1576-25.28970.20481470.18032708X-RAY DIFFRACTION96

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