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Basic information

Entry
Database: PDB / ID: 2xen
TitleStructural Determinants for Improved Thermal Stability of Designed Ankyrin Repeat Proteins With a Redesigned C-capping Module.
ComponentsNI1C MUT4
KeywordsDE NOVO PROTEIN / PROTEIN ENGINEERING / REPEAT PROTEIN / ANKYRIN / DESIGN / PROTEIN-PROTEIN INTERACTION
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / METHANOL
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.2 Å
AuthorsKramer, M. / Wetzel, S.K. / Pluckthun, A. / Mittl, P. / Grutter, M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural Determinants for Improved Thermal Stability of Designed Ankyrin Repeat Proteins with a Redesigned C-Capping Module.
Authors: Kramer, M. / Wetzel, S.K. / Pluckthun, A. / Mittl, P. / Grutter, M.
History
DepositionMay 17, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: NI1C MUT4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9184
Polymers9,7281
Non-polymers1903
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.150, 35.330, 32.400
Angle α, β, γ (deg.)90.00, 114.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2028-

HOH

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Components

#1: Protein NI1C MUT4


Mass: 9727.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.48 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→31 Å / Num. obs: 4117 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 19.51 Å2 / Rmerge(I) obs: 0.06

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.2→29.499 Å / SU ML: 0.37 / σ(F): 1.36 / Phase error: 25.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 407 9.9 %
Rwork0.1681 --
obs0.1737 4113 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.541 Å2 / ksol: 0.411 e/Å3
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1-13.3944 Å2-0 Å29.266 Å2
2---6.4351 Å20 Å2
3----6.9594 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms682 0 11 47 740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008700
X-RAY DIFFRACTIONf_angle_d0.944941
X-RAY DIFFRACTIONf_dihedral_angle_d15.763259
X-RAY DIFFRACTIONf_chiral_restr0.06108
X-RAY DIFFRACTIONf_plane_restr0.003126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2005-2.51880.24741400.18091231X-RAY DIFFRACTION99
2.5188-3.17280.22411330.16351215X-RAY DIFFRACTION100
3.1728-29.50150.20481340.1641260X-RAY DIFFRACTION99

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