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- PDB-4uot: Thermodynamic hyperstability in parametrically designed helical b... -

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Basic information

Entry
Database: PDB / ID: 4uot
TitleThermodynamic hyperstability in parametrically designed helical bundles
ComponentsDESIGNED HELICAL BUNDLE 5H2L
KeywordsDE NOVO PROTEIN / PROTEIN DESIGN / THERMODYNAMIC HYPERSTABILITY HELICAL BUNDLE
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsOberdorfer, G. / Huang, P. / Pei, X.Y. / Xu, C. / Gonen, T. / Nannenga, B. / DiMaio, D. / Rogers, J. / Luisi, B.F. / Baker, D.
CitationJournal: Science / Year: 2014
Title: High Thermodynamic Stability of Parametrically Designed Helical Bundles
Authors: Huang, P. / Oberdorfer, G. / Xu, C. / Pei, X.Y. / Nannenga, B.L. / Rogers, J.M. / Dimaio, F. / Gonen, T. / Luisi, B. / Baker, D.
History
DepositionJun 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn
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_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DESIGNED HELICAL BUNDLE 5H2L
B: DESIGNED HELICAL BUNDLE 5H2L
C: DESIGNED HELICAL BUNDLE 5H2L
D: DESIGNED HELICAL BUNDLE 5H2L
E: DESIGNED HELICAL BUNDLE 5H2L


Theoretical massNumber of molelcules
Total (without water)20,6805
Polymers20,6805
Non-polymers00
Water6,071337
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9760 Å2
ΔGint-93 kcal/mol
Surface area9490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.400, 88.020, 103.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-2034-

HOH

21E-2001-

HOH

31E-2048-

HOH

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Components

#1: Protein/peptide
DESIGNED HELICAL BUNDLE 5H2L


Mass: 4136.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsN-TERMINAL THR HAS ACETYLATION, C-TERMINAL GLN HAS AMIDATION.

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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: 3.41 Å3/Da / Density % sol: 63.9 % / Description: NONE
Crystal growpH: 5.6
Details: 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE PH 5.6 AND 25 % W/V PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.03978
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03978 Å / Relative weight: 1
ReflectionResolution: 1.69→35 Å / Num. obs: 11034 / % possible obs: 99.6 % / Observed criterion σ(I): 2.5 / Redundancy: 5.3 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.5
Reflection shellResolution: 1.69→1.73 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ROSETTA MODEL

Resolution: 1.69→24.433 Å / SU ML: 0.15 / σ(F): 0.08 / Phase error: 19.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1845 2728 5 %
Rwork0.1782 --
obs0.1785 54653 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0.57 Å2
Displacement parametersBiso mean: 22.49 Å2
Refinement stepCycle: LAST / Resolution: 1.69→24.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1440 0 0 337 1777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0241482
X-RAY DIFFRACTIONf_angle_d1.7691942
X-RAY DIFFRACTIONf_dihedral_angle_d14.906645
X-RAY DIFFRACTIONf_chiral_restr0.099231
X-RAY DIFFRACTIONf_plane_restr0.007226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.72070.27821660.28082717X-RAY DIFFRACTION100
1.7207-1.75380.26981360.27562747X-RAY DIFFRACTION100
1.7538-1.78960.28531400.26622775X-RAY DIFFRACTION100
1.7896-1.82850.23671930.24482622X-RAY DIFFRACTION100
1.8285-1.8710.28141570.2462764X-RAY DIFFRACTION100
1.871-1.91780.21331470.2312747X-RAY DIFFRACTION100
1.9178-1.96960.24051800.22212685X-RAY DIFFRACTION100
1.9696-2.02760.23091520.20782729X-RAY DIFFRACTION100
2.0276-2.0930.22481520.19312746X-RAY DIFFRACTION100
2.093-2.16770.19941500.17032725X-RAY DIFFRACTION100
2.1677-2.25450.204990.16992788X-RAY DIFFRACTION100
2.2545-2.3570.20551170.16132760X-RAY DIFFRACTION100
2.357-2.48110.17741290.16052737X-RAY DIFFRACTION100
2.4811-2.63640.1971290.17462751X-RAY DIFFRACTION100
2.6364-2.83970.19061360.17852740X-RAY DIFFRACTION100
2.8397-3.1250.18771440.17852734X-RAY DIFFRACTION100
3.125-3.57590.13241280.14582736X-RAY DIFFRACTION99
3.5759-4.50070.10761470.13062718X-RAY DIFFRACTION99
4.5007-24.43510.20131260.19972704X-RAY DIFFRACTION98

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