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- PDB-2qyj: Crystal structure of a designed full consensus ankyrin -

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Basic information

Entry
Database: PDB / ID: 2qyj
TitleCrystal structure of a designed full consensus ankyrin
Componentsankyrin NI3C
KeywordsDE NOVO PROTEIN / ankyrin repeat / repeat protein / helix-turn-helix-Beta-turn
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsMerz, T.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Stabilizing ionic interactions in a full-consensus ankyrin repeat protein.
Authors: Merz, T. / Wetzel, S.K. / Firbank, S. / Pluckthun, A. / Grutter, M.G. / Mittl, P.R.E.
History
DepositionAug 15, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 2, 2014Group: Database references
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: ankyrin NI3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3105
Polymers17,9261
Non-polymers3844
Water2,000111
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.480, 74.480, 50.990
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein ankyrin NI3C


Mass: 17926.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.7M (NH4)2SO4, 0.1M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 14, 2005 / Details: mirror
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2→64.55 Å / Num. obs: 10232 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.68 % / Biso Wilson estimate: 31.966 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.073 / Net I/σ(I): 21.44
Reflection shellResolution: 2→2.1 Å / Redundancy: 7.16 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 6.2 / Num. measured obs: 5165 / Num. unique obs: 721 / Rsym value: 0.364 / % possible all: 48.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
AMoREphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MJO

1mjo


Resolution: 2.05→64.55 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.768 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.21 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 493 4.8 %RANDOM
Rwork0.186 ---
all0.188 10232 --
obs0.188 10204 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.279 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20.51 Å20 Å2
2--1.02 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.05→64.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1161 0 20 111 1292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221207
X-RAY DIFFRACTIONr_angle_refined_deg1.1091.9971629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7985153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10226.10259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19715219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.793156
X-RAY DIFFRACTIONr_chiral_restr0.0670.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02896
X-RAY DIFFRACTIONr_nbd_refined0.220.2619
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2833
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.287
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.217
X-RAY DIFFRACTIONr_mcbond_it0.6421.5779
X-RAY DIFFRACTIONr_mcangle_it1.10621199
X-RAY DIFFRACTIONr_scbond_it1.8893461
X-RAY DIFFRACTIONr_scangle_it2.9314.5430
LS refinement shellResolution: 2.05→2.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 36 -
Rwork0.231 729 -
all-765 -
obs--100 %

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