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- PDB-5j2l: De novo design of protein homo-oligomers with modular hydrogen bo... -

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Basic information

Entry
Database: PDB / ID: 5j2l
TitleDe novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity
Componentsprotein design 2L4HC2_11
KeywordsDE NOVO PROTEIN / rosetta / de novo design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _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
B: protein design 2L4HC2_11
A: protein design 2L4HC2_11


Theoretical massNumber of molelcules
Total (without water)19,9692
Polymers19,9692
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-24 kcal/mol
Surface area9360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.380, 45.700, 48.320
Angle α, β, γ (deg.)90.00, 97.43, 90.00
Int Tables number4
Space group name H-MP1211
DetailsDimer according to gel filtration, SEC-MALS, and small-angle x-ray scattering (SAXS)

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Components

#1: Protein protein design 2L4HC2_11


Mass: 9984.396 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.: 80 / 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: 1.94 Å3/Da / Density % sol: 36.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.5 and 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 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→35.08 Å / Num. obs: 11050 / % possible obs: 99.4 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 23.1

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Processing

Software
NameVersionClassification
PHENIXdev_1616refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→35.08 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 24.74
RfactorNum. reflection% reflection
Rfree0.2419 1105 10 %
Rwork0.2058 --
obs0.2094 11049 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.96→35.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1332 0 0 80 1412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131332
X-RAY DIFFRACTIONf_angle_d1.1261762
X-RAY DIFFRACTIONf_dihedral_angle_d12.442592
X-RAY DIFFRACTIONf_chiral_restr0.063196
X-RAY DIFFRACTIONf_plane_restr0.005232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9601-2.04940.3291360.25931223X-RAY DIFFRACTION99
2.0494-2.15740.2411360.20941232X-RAY DIFFRACTION99
2.1574-2.29250.24521390.19861237X-RAY DIFFRACTION99
2.2925-2.46950.26091370.19431229X-RAY DIFFRACTION100
2.4695-2.71790.26991390.20321256X-RAY DIFFRACTION100
2.7179-3.1110.27051370.21631245X-RAY DIFFRACTION100
3.111-3.91870.21461390.19011257X-RAY DIFFRACTION100
3.9187-35.08850.22331420.21141265X-RAY DIFFRACTION98

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