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- PDB-7dns: Crystal structure of domain-swapped dimer of H5_Fold-0 Elsa; de n... -

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Basic information

Entry
Database: PDB / ID: 7dns
TitleCrystal structure of domain-swapped dimer of H5_Fold-0 Elsa; de novo designed protein with an asymmetric all-alpha topology
Componentsde novo designed protein
KeywordsDE NOVO PROTEIN / Computational Design / All-alpha protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.327 Å
AuthorsSuzuki, K. / Kobayashi, N. / Murata, T. / Sakuma, K. / Kosugi, T. / Koga, R. / Koga, N.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: Design of complicated all-alpha protein structures
Authors: Sakuma, K. / Kobayashi, N. / Sugiki, T. / Nagashima, T. / Fujiwara, T. / Suzuki, K. / Kobayashi, N. / Murata, T. / Kosugi, T. / Koga, R. / Koga, N.
History
DepositionDec 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 2.0Oct 6, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Experimental preparation / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_ref_seq / struct_site_gen
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_site_gen.label_seq_id
Revision 2.1Nov 1, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 2.2Jan 10, 2024Group: Database references / Category: citation / citation_author / Item: _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: de novo designed protein
B: de novo designed protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4973
Polymers22,4052
Non-polymers921
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-20 kcal/mol
Surface area9790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.980, 33.660, 58.380
Angle α, β, γ (deg.)90.000, 93.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein de novo designed protein


Mass: 11202.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.4 M MgCl2, 0.1 M Tris (pH 7.5), 30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.327→45.912 Å / Num. obs: 7770 / % possible obs: 98.7 % / Redundancy: 6.41 % / Biso Wilson estimate: 41.7 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.097 / Net I/σ(I): 13.63
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.33-2.474.480.4832.5411470.8710.54892.3
2.47-2.646.130.3624.4211680.9490.39699.8
2.64-2.857.060.2517.0211140.9750.271100
2.85-3.127.080.16711.1410080.9870.1899.9
3.12-3.497.060.1116.319290.9930.119100
3.49-4.027.940.07521.688200.9960.08299.9
4.02-4.916.280.05726.627030.9960.06599.9
4.91-6.916.960.06128.575520.9950.066100
6.91-45.916.520.05234.533290.9970.05699.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
MOLREPphasing
PHENIX1.12refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.327→45.912 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 30.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2469 389 5.01 %
Rwork0.2066 7378 -
obs0.2086 7767 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.28 Å2 / Biso mean: 57.5718 Å2 / Biso min: 22.75 Å2
Refinement stepCycle: final / Resolution: 2.327→45.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 6 16 1444
Biso mean--84.01 45.8 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031441
X-RAY DIFFRACTIONf_angle_d0.5171932
X-RAY DIFFRACTIONf_chiral_restr0.032207
X-RAY DIFFRACTIONf_plane_restr0.003262
X-RAY DIFFRACTIONf_dihedral_angle_d26.636904
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3272-2.66390.30381240.2696234796
2.6639-3.35610.29441310.23642486100
3.3561-45.9120.21611340.18082545100
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)
17.76651.2046-0.69019.561-5.01539.0646-0.09960.74230.1455-0.63310.59170.9984-0.3599-0.6366-0.42680.32330.0074-0.07410.35380.01550.47454.67511.192421.3021
22.72930.6302-0.41069.3686-1.88674.0667-0.05760.121-0.0321-0.5245-0.1113-0.50850.23180.0470.15480.2343-0.0254-0.0710.2769-0.0170.424310.2761-0.561224.65
34.60212.3253-4.61529.9175-2.59794.59550.3229-0.24640.46490.5631-0.81391.0760.1546-0.77690.39060.6115-0.2273-0.07330.5997-0.08930.65455.5428-2.817249.6599
47.6133-1.5936-0.9653.37261.62137.7453-0.0031-0.33230.96280.0663-0.1743-0.1957-0.2752-0.43180.2580.4163-0.0284-0.00960.3959-0.00690.369816.4786.445452.7474
56.1055-1.341-3.8858.63875.90869.85240.1951-0.551-0.1190.8335-0.22790.43770.15790.32690.00710.61180.01720.01980.38530.11210.35114.63290.619356.6761
62.95160.2413-0.85792.8663-5.43262.0540.13160.28840.03390.1551-0.56991.3921-0.6223-1.13050.33580.6560.03280.03230.7394-0.22440.80314.27447.385252.82
74.2716-0.3299-4.18634.29542.57698.93480.3412-0.13370.0765-0.0871-0.0264-0.105-0.76290.0004-0.21570.34970.028-0.06840.2709-0.00820.500916.75563.074733.5841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )A1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 76 )A25 - 76
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 90 )A77 - 90
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 29 )B3 - 29
5X-RAY DIFFRACTION5chain 'B' and (resid 30 through 45 )B30 - 45
6X-RAY DIFFRACTION6chain 'B' and (resid 46 through 63 )B46 - 63
7X-RAY DIFFRACTION7chain 'B' and (resid 64 through 90 )B64 - 90

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