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Basic information

Entry
Database: PDB / ID: 2xee
TitleStructural Determinants for Improved Thermal Stability of Designed Ankyrin Repeat Proteins With a Redesigned C-capping Module.
ComponentsNI3C DARPIN MUTANT5
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NI3C DARPIN MUTANT5
B: NI3C DARPIN MUTANT5
C: NI3C DARPIN MUTANT5
D: NI3C DARPIN MUTANT5


Theoretical massNumber of molelcules
Total (without water)67,1524
Polymers67,1524
Non-polymers00
Water3,153175
1
A: NI3C DARPIN MUTANT5


Theoretical massNumber of molelcules
Total (without water)16,7881
Polymers16,7881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NI3C DARPIN MUTANT5


Theoretical massNumber of molelcules
Total (without water)16,7881
Polymers16,7881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NI3C DARPIN MUTANT5


Theoretical massNumber of molelcules
Total (without water)16,7881
Polymers16,7881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NI3C DARPIN MUTANT5


Theoretical massNumber of molelcules
Total (without water)16,7881
Polymers16,7881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.050, 62.050, 270.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-2004-

HOH

21B-2011-

HOH

31B-2015-

HOH

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Components

#1: Protein
NI3C DARPIN MUTANT5


Mass: 16787.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: DESIGNED ANKYRIN REPEAT PROTEIN WITH THREE INTERNAL REPEAT AND C-TERMINAL CAPPING REPEAT TYPE MUT5.
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.24 Å3/Da / Density % sol: 45 % / 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
Reflection twinOperator: -h,-k,l / Fraction: 0.382
ReflectionResolution: 2.1→50 Å / Num. obs: 35848 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 5.63 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.09

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QYJ

2qyj


Resolution: 2.1→49.931 Å / SU ML: 0 / σ(F): 1.36 / Phase error: 36.47 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.24 2034 5.7 %
Rwork0.1753 --
obs0.1788 35848 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.962 Å2 / ksol: 0.397 e/Å3
Displacement parametersBiso mean: 0 Å2
Baniso -1Baniso -2Baniso -3
1--7.3526 Å20 Å20 Å2
2---7.3526 Å20 Å2
3---14.7052 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4720 0 0 175 4895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024800
X-RAY DIFFRACTIONf_angle_d0.466486
X-RAY DIFFRACTIONf_dihedral_angle_d13.7681774
X-RAY DIFFRACTIONf_chiral_restr0.028746
X-RAY DIFFRACTIONf_plane_restr0.001870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.14050.29641050.28961791X-RAY DIFFRACTION98
2.1405-2.18420.27231050.26011742X-RAY DIFFRACTION98
2.1842-2.23170.3061050.24431824X-RAY DIFFRACTION98
2.2317-2.28360.29411090.26381799X-RAY DIFFRACTION98
2.2836-2.34070.28831060.23561791X-RAY DIFFRACTION98
2.3407-2.4040.22941090.2081854X-RAY DIFFRACTION98
2.404-2.47470.26191140.21021870X-RAY DIFFRACTION98
2.4747-2.55460.26471080.21491840X-RAY DIFFRACTION98
2.5546-2.64590.30641090.19691865X-RAY DIFFRACTION98
2.6459-2.75180.20381130.20991881X-RAY DIFFRACTION98
2.7518-2.8770.25651130.19761899X-RAY DIFFRACTION98
2.877-3.02870.28171080.19251892X-RAY DIFFRACTION98
3.0287-3.21840.23431120.17521911X-RAY DIFFRACTION98
3.2184-3.46690.22471170.16111921X-RAY DIFFRACTION98
3.4669-3.81560.22761120.13561921X-RAY DIFFRACTION98
3.8156-4.36750.18541180.12711937X-RAY DIFFRACTION98
4.3675-5.50150.21191180.14031983X-RAY DIFFRACTION98
5.5015-49.94560.24591250.15142121X-RAY DIFFRACTION98

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