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- PDB-6z0l: Het-N2 - De novo designed three-helix heterodimer with Cysteine a... -

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Basic information

Entry
Database: PDB / ID: 6z0l
TitleHet-N2 - De novo designed three-helix heterodimer with Cysteine at the N2 position of the alpha-helix
Components
  • Cys-N2 Strand
  • Positive Strand
KeywordsDE NOVO PROTEIN / Acyl Transfer Activity / Domain Swapped Dimer / Oxyanion-Binding Site
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.33 Å
AuthorsMcEwen, A.G. / Poussin-Courmontagne, P. / Naudin, E.A. / DeGrado, W.F. / Torbeev, V.
Funding supportEuropean Union, France, 3items
OrganizationGrant numberCountry
European Research Council (ERC)715062-HiChemSynProEuropean Union
French National Research AgencyANR-10-LABX-0026_CSC France
French National Research AgencyANR-10-INBS-05 France
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Acyl Transfer Catalytic Activity in De Novo Designed Protein with N-Terminus of alpha-Helix As Oxyanion-Binding Site.
Authors: Naudin, E.A. / McEwen, A.G. / Tan, S.K. / Poussin-Courmontagne, P. / Schmitt, J.L. / Birck, C. / DeGrado, W.F. / Torbeev, V.
History
DepositionMay 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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
Revision 1.3Nov 6, 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: Positive Strand
B: Cys-N2 Strand
C: Positive Strand
D: Cys-N2 Strand
E: Positive Strand
F: Cys-N2 Strand
G: Positive Strand
H: Cys-N2 Strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,73514
Polymers43,1508
Non-polymers5856
Water1,53185
1
A: Positive Strand
B: Cys-N2 Strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0124
Polymers10,7872
Non-polymers2252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-25 kcal/mol
Surface area5910 Å2
MethodPISA
2
C: Positive Strand
D: Cys-N2 Strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0355
Polymers10,7872
Non-polymers2483
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-36 kcal/mol
Surface area5960 Å2
MethodPISA
3
E: Positive Strand
F: Cys-N2 Strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9003
Polymers10,7872
Non-polymers1121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-26 kcal/mol
Surface area6090 Å2
MethodPISA
4
G: Positive Strand
H: Cys-N2 Strand


Theoretical massNumber of molelcules
Total (without water)10,7872
Polymers10,7872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-23 kcal/mol
Surface area6220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.669, 49.952, 53.043
Angle α, β, γ (deg.)105.090, 92.490, 110.150
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
Positive Strand


Mass: 5462.353 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein/peptide
Cys-N2 Strand


Mass: 5325.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% PEG 400, 0.1 M cadmium chloride, 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 20, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.17→37.77 Å / Num. obs: 14582 / % possible obs: 73.8 % / Redundancy: 3.283 % / Biso Wilson estimate: 53.737 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.257 / Rrim(I) all: 0.307 / Χ2: 1.19 / Net I/σ(I): 2.97 / Num. measured all: 47878
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.462.9882.5880.3421330.2223.11471.6
2.46-2.663.2851.7740.5726090.4362.1292.4
2.66-2.913.2661.2530.8723350.6011.49890.5
2.91-3.253.2380.6561.7219930.8650.78586.1
3.25-3.753.2760.2663.9817380.9580.31884.3
3.75-4.593.4040.1716.4116870.9720.20498.1
4.59-6.463.5920.1576.7613270.9770.18598.5
6.46-37.773.5460.08112.077430.9930.09598

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.1_rc3refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G6U

1g6u


Resolution: 2.33→37.77 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 27.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.283 486 5.56 %
Rwork0.2228 8248 -
obs0.2263 8734 54.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.1 Å2 / Biso mean: 34.1864 Å2 / Biso min: 2.52 Å2
Refinement stepCycle: final / Resolution: 2.33→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 5 85 3120
Biso mean--36.8 23.05 -
Num. residues----401
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.33-2.670.3491430.261587992217
2.67-3.360.31611510.24412727287854
3.37-37.770.26692920.21034642493493
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.0019-0.0034-0.00080.0078-0.00550.03190.0266-0.0367-0.00780.08560.02950.001-0.0074-0.00030.04090.2076-0.084-0.01130.06480.10680.214-29.0266.0367-12.31
20.0017-0.0095-0.00070.0029-0.00920.0009-0.0083-0.0082-0.0217-0.0022-0.02020.02230.0015-0.0398-0.02230.0532-0.0848-0.08110.1184-0.02510.2083-42.092610.1966-15.4167
30.07540.0061-0.0180.00380.00320.01150.0162-0.075-0.04260.03930.00370.03360.0107-0.01440.05030.08530.09480.19760.02880.0429-0.0425-53.85174.4031-45.5549
40.0181-0.0247-0.01820.030.00460.0875-0.0299-0.00680.01830.0603-0.0103-0.01030.03410.012-0.08850.1532-0.0447-0.05090.0832-0.00870.0897-46.6314-2.0596-34.8187
50.0687-0.01620.08930.0097-0.02820.122-0.0562-0.00310.0057-0.0317-0.08380.0478-0.01620.0295-0.05950.14980.07990.05460.07320.01220.1034-39.6366-9.6594-54.9502
60.0075-0.0098-0.01170.00840.00710.001-0.03960.0236-0.00310.0108-0.007-0.00720.01090.0411-0.0440.0148-0.01210.13260.03020.1740.1531-32.46391.8859-51.4748
70.02110.00070.01620.00820.01410.04040.01910.01910.01580.01810.01030.0201-0.03340.04160.00760.30710.07030.01570.0034-0.02190.025-26.755725.8446-21.5058
80.0304-0.01790.01960.0465-0.01560.0162-0.0417-0.05290.01020.0351-0.01320.0286-0.0284-0.0254-0.14410.07120.11130.07210.00940.15180.0467-28.667316.5654-32.5534
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 48)A0 - 48
2X-RAY DIFFRACTION2(chain 'B' and resid 0 through 48)B0 - 48
3X-RAY DIFFRACTION3(chain 'C' and resid 0 through 48)C0 - 48
4X-RAY DIFFRACTION4(chain 'D' and resid 0 through 48)D0 - 48
5X-RAY DIFFRACTION5(chain 'E' and resid 0 through 48)E0 - 48
6X-RAY DIFFRACTION6(chain 'F' and resid 0 through 48)F0 - 48
7X-RAY DIFFRACTION7(chain 'G' and resid 0 through 48)G0 - 48
8X-RAY DIFFRACTION8(chain 'H' and resid 0 through 48)H0 - 48

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