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- PDB-6z0m: Het-Ncap - De novo designed three-helix heterodimer with Cysteine... -

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Basic information

Entry
Database: PDB / ID: 6z0m
TitleHet-Ncap - De novo designed three-helix heterodimer with Cysteine at the Ncap position of the alpha-helix
Components
  • Cys-Ncap strand
  • Positive Strand
KeywordsDE NOVO PROTEIN / Acyl Transfer Activity / Domain Swapped Dimer / Oxyanion-Binding Site
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 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 20, 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-Ncap strand
C: Positive Strand
D: Cys-Ncap strand
E: Positive Strand
F: Cys-Ncap strand
G: Positive Strand
H: Cys-Ncap strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,36710
Polymers43,2068
Non-polymers1612
Water11,061614
1
A: Positive Strand
B: Cys-Ncap strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8973
Polymers10,8012
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-12 kcal/mol
Surface area5490 Å2
MethodPISA
2
C: Positive Strand
D: Cys-Ncap strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8673
Polymers10,8012
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-17 kcal/mol
Surface area5500 Å2
MethodPISA
3
E: Positive Strand
F: Cys-Ncap strand


Theoretical massNumber of molelcules
Total (without water)10,8012
Polymers10,8012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-29 kcal/mol
Surface area5600 Å2
MethodPISA
4
G: Positive Strand
H: Cys-Ncap strand


Theoretical massNumber of molelcules
Total (without water)10,8012
Polymers10,8012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-15 kcal/mol
Surface area5510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.875, 73.097, 84.128
Angle α, β, γ (deg.)90.000, 105.020, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-285-

HOH

21C-178-

HOH

31D-222-

HOH

41D-256-

HOH

51G-194-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 or resid 2 through 5...
21(chain B and (resid 0 or resid 2 through 5...
31(chain C and (resid 0 or resid 2 through 5...
41(chain D and (resid 0 or resid 2 through 5...
51(chain E and (resid 0 or resid 2 through 5...
61(chain F and (resid 0 or resid 2 through 5...
71(chain G and (resid 0 or resid 2 through 5...
81(chain H and (resid 0 or resid 2 through 5...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 0 or resid 2 through 5...A0
121(chain A and (resid 0 or resid 2 through 5...A2 - 5
131(chain A and (resid 0 or resid 2 through 5...A9
141(chain A and (resid 0 or resid 2 through 5...A11
151(chain A and (resid 0 or resid 2 through 5...A29
161(chain A and (resid 0 or resid 2 through 5...A0 - 49
171(chain A and (resid 0 or resid 2 through 5...A37
181(chain A and (resid 0 or resid 2 through 5...A45 - 49
211(chain B and (resid 0 or resid 2 through 5...B0
221(chain B and (resid 0 or resid 2 through 5...B2 - 5
231(chain B and (resid 0 or resid 2 through 5...B9
241(chain B and (resid 0 or resid 2 through 5...B11 - 14
251(chain B and (resid 0 or resid 2 through 5...B16
261(chain B and (resid 0 or resid 2 through 5...B2932
271(chain B and (resid 0 or resid 2 through 5...B45 - 49
311(chain C and (resid 0 or resid 2 through 5...C0
321(chain C and (resid 0 or resid 2 through 5...C2 - 5
331(chain C and (resid 0 or resid 2 through 5...C9
341(chain C and (resid 0 or resid 2 through 5...C11
351(chain C and (resid 0 or resid 2 through 5...C29
361(chain C and (resid 0 or resid 2 through 5...C0 - 49
371(chain C and (resid 0 or resid 2 through 5...C37
381(chain C and (resid 0 or resid 2 through 5...C45 - 49
411(chain D and (resid 0 or resid 2 through 5...D0
421(chain D and (resid 0 or resid 2 through 5...D2 - 5
431(chain D and (resid 0 or resid 2 through 5...D9
441(chain D and (resid 0 or resid 2 through 5...D11
451(chain D and (resid 0 or resid 2 through 5...D29
461(chain D and (resid 0 or resid 2 through 5...D0 - 49
471(chain D and (resid 0 or resid 2 through 5...D37
481(chain D and (resid 0 or resid 2 through 5...D45 - 49
511(chain E and (resid 0 or resid 2 through 5...E0
521(chain E and (resid 0 or resid 2 through 5...E2 - 5
531(chain E and (resid 0 or resid 2 through 5...E9
541(chain E and (resid 0 or resid 2 through 5...E11
551(chain E and (resid 0 or resid 2 through 5...E29
561(chain E and (resid 0 or resid 2 through 5...E0 - 49
571(chain E and (resid 0 or resid 2 through 5...E37
581(chain E and (resid 0 or resid 2 through 5...E45 - 49
611(chain F and (resid 0 or resid 2 through 5...F0
621(chain F and (resid 0 or resid 2 through 5...F2 - 5
631(chain F and (resid 0 or resid 2 through 5...F9
641(chain F and (resid 0 or resid 2 through 5...F11
651(chain F and (resid 0 or resid 2 through 5...F29
661(chain F and (resid 0 or resid 2 through 5...F0 - 49
671(chain F and (resid 0 or resid 2 through 5...F37
681(chain F and (resid 0 or resid 2 through 5...F45 - 49
711(chain G and (resid 0 or resid 2 through 5...G0
721(chain G and (resid 0 or resid 2 through 5...G2 - 5
731(chain G and (resid 0 or resid 2 through 5...G9
741(chain G and (resid 0 or resid 2 through 5...G11
751(chain G and (resid 0 or resid 2 through 5...G29
761(chain G and (resid 0 or resid 2 through 5...G0 - 49
771(chain G and (resid 0 or resid 2 through 5...G37
781(chain G and (resid 0 or resid 2 through 5...G45 - 49
811(chain H and (resid 0 or resid 2 through 5...H0
821(chain H and (resid 0 or resid 2 through 5...H2 - 5
831(chain H and (resid 0 or resid 2 through 5...H9
841(chain H and (resid 0 or resid 2 through 5...H11
851(chain H and (resid 0 or resid 2 through 5...H29
861(chain H and (resid 0 or resid 2 through 5...H0 - 49
871(chain H and (resid 0 or resid 2 through 5...H37
881(chain H and (resid 0 or resid 2 through 5...H45 - 49

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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-Ncap strand


Mass: 5339.072 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.64 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 550 MME, 0.01 M zinc sulfate, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.45→81.25 Å / Num. obs: 78983 / % possible obs: 99.3 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.023 / Rrim(I) all: 0.042 / Net I/σ(I): 12.6 / Num. measured all: 265700 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.45-1.473.30.8631303539370.7210.5561.0311.399.2
7.94-81.253.50.02717785110.9980.0170.03241.798.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.44 Å47.99 Å
Translation1.44 Å47.99 Å

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Processing

Software
NameVersionClassification
PHENIX1.18rc3refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.7.18phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G6U

1g6u


Resolution: 1.45→81.25 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2068 4028 5.1 %
Rwork0.1522 74903 -
obs0.1549 78931 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.3 Å2 / Biso mean: 35.4263 Å2 / Biso min: 13.12 Å2
Refinement stepCycle: final / Resolution: 1.45→81.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 6 622 3668
Biso mean--54.91 45.32 -
Num. residues----400
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A720X-RAY DIFFRACTION9.481TORSIONAL
12B720X-RAY DIFFRACTION9.481TORSIONAL
13C720X-RAY DIFFRACTION9.481TORSIONAL
14D720X-RAY DIFFRACTION9.481TORSIONAL
15E720X-RAY DIFFRACTION9.481TORSIONAL
16F720X-RAY DIFFRACTION9.481TORSIONAL
17G720X-RAY DIFFRACTION9.481TORSIONAL
18H720X-RAY DIFFRACTION9.481TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.470.32151420.27172584272699
1.47-1.480.26881240.24612583270799
1.48-1.50.2811260.22222568269499
1.5-1.520.27771390.20022538267799
1.52-1.540.24731490.19662580272999
1.54-1.570.23681500.180925932743100
1.57-1.590.23751370.156625912728100
1.59-1.610.20341250.152726162741100
1.61-1.640.19391470.151925442691100
1.64-1.670.23411630.15342560272399
1.67-1.70.21811530.14842580273399
1.7-1.730.2191290.156625732702100
1.73-1.770.28471270.16982605273299
1.77-1.810.27911460.16842526267299
1.81-1.850.2331520.147926312783100
1.85-1.890.19621340.13926102744100
1.89-1.950.17121550.12925392694100
1.95-20.20731310.127726062737100
2-2.070.18691540.13872577273199
2.07-2.140.19051260.13525912717100
2.14-2.230.19561500.12512582273299
2.23-2.330.17231350.11832578271399
2.33-2.450.17921460.11922581272799
2.45-2.610.21531190.13242585270499
2.61-2.810.19531290.14792619274899
2.81-3.090.19521420.14722554269699
3.09-3.540.21161300.14862584271498
3.54-4.450.2051320.14582608274099
4.45-81.250.21031360.20172617275398

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