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- PDB-5cy5: Crystal structure of the T33-51H designed self-assembling protein... -

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Basic information

Entry
Database: PDB / ID: 5cy5
TitleCrystal structure of the T33-51H designed self-assembling protein tetrahedron
Components
  • T33-51H-A
  • T33-51H-B
KeywordsDE NOVO PROTEIN / BIONANOTECHNOLOGY / SYMMETRY / BIOMATERIALS / TETRAHEDRAL / COMPUTATIONAL DESIGN / ROSETTA / SELF-ASSEMBLY / NANOMATERIAL / SOLUBILITY
Function / homologyHypothetical Protein Ta1238; Chain: A; / Cobalamin adenosyltransferase-like / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesThermoplasma acidophilum (acidophilic)
Pyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.4 Å
AuthorsCannon, K.A. / Cascio, D. / Park, R. / Boyken, S. / King, N. / Yeates, T.O.
CitationJournal: Protein Sci. / Year: 2020
Title: Design and structure of two new protein cages illustrate successes and ongoing challenges in protein engineering.
Authors: Cannon, K.A. / Park, R.U. / Boyken, S.E. / Nattermann, U. / Yi, S. / Baker, D. / King, N.P. / Yeates, T.O.
History
DepositionJul 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: T33-51H-B
A: T33-51H-A


Theoretical massNumber of molelcules
Total (without water)40,3762
Polymers40,3762
Non-polymers00
Water00
1
B: T33-51H-B
A: T33-51H-A
x 12


Theoretical massNumber of molelcules
Total (without water)484,50924
Polymers484,50924
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area53000 Å2
ΔGint-266 kcal/mol
Surface area135130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.700, 106.700, 106.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23

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Components

#1: Protein T33-51H-B


Mass: 21031.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Plasmid: pET29b / Production host: Escherichia coli (E. coli)
#2: Protein T33-51H-A


Mass: 19344.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET29b / Production host: Escherichia coli (E. coli)

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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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 8.8 / Details: 100 mM HEPES pH 8.8 and 15 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.4→75.448 Å / Num. obs: 5827 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Rmerge F obs: 1 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.094 / Χ2: 0.992 / Net I/σ(I): 29.04 / Num. measured all: 154895
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.4-3.480.7041.3592.79107844304281.38899.5
3.48-3.580.9090.9254.63116544154150.942100
3.58-3.680.9480.6186.9111114044040.629100
3.68-3.80.9680.5298.11102353803800.539100
3.8-3.920.980.40410.5995013743740.412100
3.92-4.060.9930.26215.92105453673670.267100
4.06-4.210.9940.18622.9199383563560.189100
4.21-4.380.9960.16325.9795263443440.166100
4.38-4.580.9970.12632.5887593283280.129100
4.58-4.80.9980.12132.3776183083080.123100
4.8-5.060.9980.11534.7883693073070.117100
5.06-5.370.9980.11135.1978372842840.113100
5.37-5.740.9990.10835.6871552632630.11100
5.74-6.20.9980.10735.5266092522520.109100
6.2-6.7910.06850.5659812332330.069100
6.79-7.5910.05168.1957052142140.052100
7.59-8.7710.0481.3948501911910.041100
8.77-10.7410.03684.1838771671670.036100
10.74-15.1910.03486.9432451311310.035100
15.1910.03878.16159682810.03998.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1nog, 1wy1

1nog

1wy1


Resolution: 3.4→75.448 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.18 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1971 583 10.01 %RANDOM
Rwork0.156 5241 --
obs0.1616 5825 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.48 Å2 / Biso mean: 81.1072 Å2 / Biso min: 42.68 Å2
Refinement stepCycle: final / Resolution: 3.4→75.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 0 0 2255
Num. residues----286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082281
X-RAY DIFFRACTIONf_angle_d0.9953069
X-RAY DIFFRACTIONf_chiral_restr0.034361
X-RAY DIFFRACTIONf_plane_restr0.003388
X-RAY DIFFRACTIONf_dihedral_angle_d16.521871
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 90 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.4-3.73990.23041430.178412881431
3.7399-4.2810.19091430.157112871430
4.281-5.39310.20211450.157213041449
5.3931-61.61340.19561520.149913621514
Refinement TLS params.Method: refined / Origin x: 32.276 Å / Origin y: -31.569 Å / Origin z: -0.238 Å
111213212223313233
T0.4085 Å20.0804 Å2-0.0451 Å2-0.637 Å2-0.0254 Å2--0.6128 Å2
L-0.1938 °20.4041 °2-0.62 °2-0.6057 °20.0164 °2--7.6424 °2
S0.042 Å °0.0467 Å °-0.0169 Å °-0.1152 Å °-0.1144 Å °0.0578 Å °0.058 Å °0.3352 Å °-0.0459 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 24:166 ) OR ( CHAIN B AND RESID 23:171 )A24 - 166
2X-RAY DIFFRACTION1( CHAIN A AND RESID 24:166 ) OR ( CHAIN B AND RESID 23:171 )B23 - 171

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