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

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Basic information

Entry
Database: PDB / ID: 4uos
TitleThermodynamic hyperstability in parametrically designed helical bundles
ComponentsDESIGNED HELICAL BUNDLE
KeywordsDE NOVO PROTEIN / PROTEIN DESIGN / THERMODYNAMIC HYPERSTABILITY HELICAL BUNDLE
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.63 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 1.2Dec 14, 2016Group: Data collection
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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: DESIGNED HELICAL BUNDLE


Theoretical massNumber of molelcules
Total (without water)22,4401
Polymers22,4401
Non-polymers00
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.460, 72.150, 51.260
Angle α, β, γ (deg.)90.00, 92.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DESIGNED HELICAL BUNDLE


Mass: 22439.832 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) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2PLYSS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST TWO AMINO ACIDS, MG, RESULT FROM CLONING. LAST TWO AMINO ACIDS, GW, ARE NOT BEEN SEE IN THE ...FIRST TWO AMINO ACIDS, MG, RESULT FROM CLONING. LAST TWO AMINO ACIDS, GW, ARE NOT BEEN SEE IN THE ELECTRON DENSITY

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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: 2.7 Å3/Da / Density % sol: 52.72 % / Description: NONE
Crystal growpH: 7.4 / Details: 0.2 M AMMONIUM SULFATE, 10% W/V PEG 4000, pH 7.4

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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 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03978 Å / Relative weight: 1
ReflectionResolution: 1.63→50.7 Å / Num. obs: 28658 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.6
Reflection shellResolution: 1.63→1.68 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.8 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
iMOSFLMdata reduction
Aimlessdata scaling
ACORNphasing
RefinementMethod to determine structure: AB INITIO PHASING
Starting model: NONE

Resolution: 1.63→23.596 Å / SU ML: 0.14 / σ(F): 1.36 / Phase error: 22.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2064 1257 4.8 %
Rwork0.1931 --
obs0.1938 26048 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→23.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 0 302 1824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0281561
X-RAY DIFFRACTIONf_angle_d1.8922049
X-RAY DIFFRACTIONf_dihedral_angle_d18.483701
X-RAY DIFFRACTIONf_chiral_restr0.14240
X-RAY DIFFRACTIONf_plane_restr0.006243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.69520.27381300.23642794X-RAY DIFFRACTION99
1.6952-1.77240.26681530.22032814X-RAY DIFFRACTION99
1.7724-1.86580.24291590.22822765X-RAY DIFFRACTION99
1.8658-1.98260.34411250.28792716X-RAY DIFFRACTION96
1.9826-2.13560.23091390.21352798X-RAY DIFFRACTION99
2.1356-2.35040.22091260.20372663X-RAY DIFFRACTION94
2.3504-2.690.19251330.19042771X-RAY DIFFRACTION97
2.69-3.38760.17451260.17322712X-RAY DIFFRACTION96
3.3876-23.59890.18631660.16972758X-RAY DIFFRACTION97

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