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- PDB-4tql: Computationally designed three helix bundle -

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Basic information

Entry
Database: PDB / ID: 4tql
TitleComputationally designed three helix bundle
ComponentsThree helix bundle
KeywordsDE NOVO PROTEIN / Helical bundle
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsNannenga, B.L. / Oberdorfer, G. / DiMaio, F. / Baker, D. / Gonen, T.
CitationJournal: Science / Year: 2014
Title: High thermodynamic stability of parametrically designed helical bundles.
Authors: Huang, P.S. / Oberdorfer, G. / Xu, C. / Pei, X.Y. / Nannenga, B.L. / Rogers, J.M. / DiMaio, F. / Gonen, T. / Luisi, B. / Baker, D.
History
DepositionJun 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Aug 26, 2015Group: Data collection / Other
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Three helix bundle
B: Three helix bundle


Theoretical massNumber of molelcules
Total (without water)59,7982
Polymers59,7982
Non-polymers00
Water1267
1
A: Three helix bundle


Theoretical massNumber of molelcules
Total (without water)29,8991
Polymers29,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Three helix bundle


Theoretical massNumber of molelcules
Total (without water)29,8991
Polymers29,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.877, 41.547, 133.202
Angle α, β, γ (deg.)98.94, 92.25, 90.06
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Three helix bundle


Mass: 29898.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris HCl, 30% Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
Reflection twinOperator: -h,k,-k-l / Fraction: 0.5
ReflectionResolution: 2.8→50 Å / Num. obs: 12173 / % possible obs: 94.2 % / Redundancy: 1.9 % / Net I/σ(I): 14.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementResolution: 2.8→43.826 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 34.01 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.31 663 5.45 %
Rwork0.2644 --
obs-12173 94.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→43.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3881 0 0 7 3888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133886
X-RAY DIFFRACTIONf_angle_d1.5695084
X-RAY DIFFRACTIONf_dihedral_angle_d19.0941736
X-RAY DIFFRACTIONf_chiral_restr0.064564
X-RAY DIFFRACTIONf_plane_restr0.006623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.08510.3041680.24222776X-RAY DIFFRACTION86
3.0851-3.52950.31781510.22942811X-RAY DIFFRACTION88
3.5295-4.43950.25351490.21512934X-RAY DIFFRACTION92
4.4395-20.57280.34631500.30932965X-RAY DIFFRACTION92

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