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- PDB-4o60: Structure of ankyrin repeat protein -

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Basic information

Entry
Database: PDB / ID: 4o60
TitleStructure of ankyrin repeat protein
ComponentsANK-N5C-317
KeywordsDE NOVO PROTEIN / ANKYRIN / DESIGNED ANKYRIN REPEATS
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsEthayathulla, A.S. / Guan, L.
CitationJournal: Sci Rep / Year: 2015
Title: A transcription blocker isolated from a designed repeat protein combinatorial library by in vivo functional screen.
Authors: Tikhonova, E.B. / Ethayathulla, A.S. / Su, Y. / Hariharan, P. / Xie, S. / Guan, L.
History
DepositionDec 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Structure summary
Revision 1.2Sep 20, 2023Group: 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

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Assembly

Deposited unit
A: ANK-N5C-317
B: ANK-N5C-317


Theoretical massNumber of molelcules
Total (without water)50,4482
Polymers50,4482
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-7 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.463, 46.801, 74.249
Angle α, β, γ (deg.)90.00, 97.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ANK-N5C-317


Mass: 25223.826 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SYNTHETIC CONSTRUCT / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 298 K / pH: 4.2
Details: 100 mM sodium acetate trihydrate (pH 4.5), 200 mM (NH3)2SO4, 16-18% PEG 4000, and 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2013 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 27744 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rsym value: 0.09 / Net I/σ(I): 30
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7 % / Rsym value: 0.7 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XEE

2xee


Resolution: 2.52→38.31 Å / SU ML: 0.33 / σ(F): 1.39 / Phase error: 25.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 1319 4.99 %
Rwork0.19 --
obs0.192 26425 98.6 %
all-27744 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.52→38.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 0 55 3503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063531
X-RAY DIFFRACTIONf_angle_d1.1214783
X-RAY DIFFRACTIONf_dihedral_angle_d15.3731287
X-RAY DIFFRACTIONf_chiral_restr0.04565
X-RAY DIFFRACTIONf_plane_restr0.006629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5239-2.6250.38511380.2542496X-RAY DIFFRACTION88
2.625-2.74440.31271540.22792839X-RAY DIFFRACTION100
2.7444-2.8890.25581460.23372805X-RAY DIFFRACTION100
2.889-3.070.3221790.23032823X-RAY DIFFRACTION100
3.07-3.30690.30591270.22422809X-RAY DIFFRACTION100
3.3069-3.63940.24911800.19332796X-RAY DIFFRACTION100
3.6394-4.16550.18081370.16512840X-RAY DIFFRACTION100
4.1655-5.2460.28811160.16692855X-RAY DIFFRACTION100
5.246-38.31430.17391420.16262843X-RAY DIFFRACTION100

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