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- PDB-5j10: De novo design of protein homo-oligomers with modular hydrogen bo... -

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Basic information

Entry
Database: PDB / ID: 5j10
TitleDe novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity
Componentspeptide design 2L4HC2_24
KeywordsDE NOVO PROTEIN / rostta / de novo design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.02 Å
AuthorsSankaran, B. / Zwart, P.H. / Pereira, J.H. / Baker, D. / Boyken, S. / Chen, Z. / Groves, B. / Langan, R.A. / Oberdorfer, G. / Ford, A. ...Sankaran, B. / Zwart, P.H. / Pereira, J.H. / Baker, D. / Boyken, S. / Chen, Z. / Groves, B. / Langan, R.A. / Oberdorfer, G. / Ford, A. / Gilmore, J. / Xu, C. / DiMaio, F. / Seelig, G.
CitationJournal: Science / Year: 2016
Title: De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity.
Authors: Boyken, S.E. / Chen, Z. / Groves, B. / Langan, R.A. / Oberdorfer, G. / Ford, A. / Gilmore, J.M. / Xu, C. / DiMaio, F. / Pereira, J.H. / Sankaran, B. / Seelig, G. / Zwart, P.H. / Baker, D.
History
DepositionMar 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: peptide design 2L4HC2_24
B: peptide design 2L4HC2_24


Theoretical massNumber of molelcules
Total (without water)18,9622
Polymers18,9622
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-32 kcal/mol
Surface area8450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.740, 42.120, 123.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsDimer according to gel filtration, SEC-MALS, and small-angle x-ray scattering (SAXS)

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Components

#1: Protein peptide design 2L4HC2_24


Mass: 9481.073 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Citric acid pH 3.5, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→61.84 Å / Num. obs: 14812 / % possible obs: 99.2 % / Redundancy: 6.8 % / Net I/σ(I): 14.7

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Processing

Software
NameVersionClassification
PHENIXdev_1616refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.02→61.835 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.31
RfactorNum. reflection% reflection
Rfree0.2517 751 5.08 %
Rwork0.2162 --
obs0.2179 14797 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.02→61.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 0 0 152 1312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041162
X-RAY DIFFRACTIONf_angle_d0.6531548
X-RAY DIFFRACTIONf_dihedral_angle_d13.541492
X-RAY DIFFRACTIONf_chiral_restr0.024190
X-RAY DIFFRACTIONf_plane_restr0.002192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0201-2.1760.25381650.21042681X-RAY DIFFRACTION97
2.176-2.3950.26051530.20852729X-RAY DIFFRACTION99
2.395-2.74160.22011340.19212797X-RAY DIFFRACTION99
2.7416-3.45410.23271380.21432858X-RAY DIFFRACTION100
3.4541-61.8640.25031610.22262981X-RAY DIFFRACTION100

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