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- PDB-2xeh: Structural Determinants for Improved Thermal Stability of Designe... -

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Basic information

Entry
Database: PDB / ID: 2xeh
TitleStructural Determinants for Improved Thermal Stability of Designed Ankyrin Repeat Proteins With a Redesigned C-capping Module.
ComponentsNI3C MUT6
KeywordsDE NOVO PROTEIN / PROTEIN ENGINEERING / PROTEIN-PROTEIN INTERACTION
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 / OTHER / Resolution: 1.81 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 14, 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

Downloads & links

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Assembly

Deposited unit
A: NI3C MUT6
B: NI3C MUT6
C: NI3C MUT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,47212
Polymers50,6073
Non-polymers8659
Water4,630257
1
A: NI3C MUT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1574
Polymers16,8691
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NI3C MUT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1574
Polymers16,8691
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NI3C MUT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1574
Polymers16,8691
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.905, 128.905, 50.696
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein NI3C MUT6


Mass: 16869.068 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli)
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.4 Å3/Da / Density % sol: 48.81 % / 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: 1.8→50 Å / Num. obs: 44196 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 25.33 Å2 / Rmerge(I) obs: 0.07

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Processing

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

Resolution: 1.81→42.194 Å / SU ML: 0.07 / σ(F): 2 / Phase error: 27.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 441 1 %
Rwork0.2168 --
obs0.2172 44196 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.645 Å2 / ksol: 0.403 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.6306 Å2-0 Å2-0 Å2
2--4.6306 Å2-0 Å2
3----9.692 Å2
Refinement stepCycle: LAST / Resolution: 1.81→42.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 45 257 3860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043667
X-RAY DIFFRACTIONf_angle_d0.8034958
X-RAY DIFFRACTIONf_dihedral_angle_d14.611347
X-RAY DIFFRACTIONf_chiral_restr0.049561
X-RAY DIFFRACTIONf_plane_restr0.004655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8061-2.06740.3151450.265414483X-RAY DIFFRACTION100
2.0674-2.60470.30421480.222414542X-RAY DIFFRACTION100
2.6047-42.20560.21021480.20214730X-RAY DIFFRACTION99

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