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- PDB-4db8: Designed Armadillo-repeat Protein -

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Basic information

Entry
Database: PDB / ID: 4db8
TitleDesigned Armadillo-repeat Protein
ComponentsArmadillo-repeat Protein
KeywordsDE NOVO PROTEIN / Solenoid repeat / Armadillo repeat
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: 2.5 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: Armadillo-repeat Protein
B: Armadillo-repeat Protein
C: Armadillo-repeat Protein
D: Armadillo-repeat Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,9138
Polymers107,8164
Non-polymers974
Water2,414134
1
A: Armadillo-repeat Protein
D: Armadillo-repeat Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9564
Polymers53,9082
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-43 kcal/mol
Surface area23310 Å2
MethodPISA
2
B: Armadillo-repeat Protein
C: Armadillo-repeat Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9564
Polymers53,9082
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-52 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.002, 113.643, 85.592
Angle α, β, γ (deg.)90.00, 106.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Armadillo-repeat Protein


Mass: 26953.939 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M magnesium chloride, 0.1 M HEPES,pH 7.5, 30% PEG 400, 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: May 21, 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: 2.5→40 Å / Num. obs: 33307 / % possible obs: 86.3 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 2.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.863 / SU B: 11.968 / SU ML: 0.273 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.845 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29885 1748 5 %RANDOM
Rwork0.23232 ---
obs0.23563 33307 95.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.128 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å20 Å20.31 Å2
2--1.45 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 4 134 7374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0227333
X-RAY DIFFRACTIONr_angle_refined_deg0.9991.9659981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1495970
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.10328.732347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.527151274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.898154
X-RAY DIFFRACTIONr_chiral_restr0.0630.21178
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215552
X-RAY DIFFRACTIONr_mcbond_it0.2991.54833
X-RAY DIFFRACTIONr_mcangle_it0.58427671
X-RAY DIFFRACTIONr_scbond_it0.80632500
X-RAY DIFFRACTIONr_scangle_it1.4874.52309
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 126 -
Rwork0.258 2167 -
obs--85.46 %

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