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- PDB-5j0k: De novo design of protein homo-oligomers with modular hydrogen bo... -

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Basic information

Entry
Database: PDB / ID: 5j0k
TitleDe novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity
Componentsdesigned protein 2L4HC2_23
KeywordsDE NOVO PROTEIN / rosetta / de novo design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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 / 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

Downloads & links

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Assembly

Deposited unit
A: designed protein 2L4HC2_23
B: designed protein 2L4HC2_23


Theoretical massNumber of molelcules
Total (without water)19,5002
Polymers19,5002
Non-polymers00
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-19 kcal/mol
Surface area8840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.720, 51.270, 65.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsDimer according to SAXS

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Components

#1: Protein designed protein 2L4HC2_23


Mass: 9750.050 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.: 248 / 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: 2.24 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Lithium chloride, 20% PEG 3,350

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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 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→27.63 Å / Num. obs: 24855 / % possible obs: 99.56 % / Redundancy: 8.5 % / Net I/σ(I): 33.3

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→27.63 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.98
RfactorNum. reflection% reflection
Rfree0.2185 1962 8.01 %
Rwork0.1989 --
obs0.2005 24485 98.07 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.8 Å
Refinement stepCycle: LAST / Resolution: 1.54→27.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1271 0 0 248 1519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031317
X-RAY DIFFRACTIONf_angle_d0.6171754
X-RAY DIFFRACTIONf_dihedral_angle_d14.824588
X-RAY DIFFRACTIONf_chiral_restr0.022197
X-RAY DIFFRACTIONf_plane_restr0.002232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5401-1.57860.27091280.24891574X-RAY DIFFRACTION97
1.5786-1.62120.25261400.24381574X-RAY DIFFRACTION97
1.6212-1.66890.26421330.23331584X-RAY DIFFRACTION97
1.6689-1.72280.27161410.22011583X-RAY DIFFRACTION99
1.7228-1.78440.25961340.22681597X-RAY DIFFRACTION99
1.7844-1.85580.26221410.23481601X-RAY DIFFRACTION98
1.8558-1.94020.29011310.27461499X-RAY DIFFRACTION93
1.9402-2.04250.241360.23251564X-RAY DIFFRACTION96
2.0425-2.17040.20721460.1891605X-RAY DIFFRACTION100
2.1704-2.33790.22621470.19091623X-RAY DIFFRACTION98
2.3379-2.5730.19291430.18431636X-RAY DIFFRACTION100
2.573-2.9450.24131410.18871657X-RAY DIFFRACTION100
2.945-3.7090.17241440.17311689X-RAY DIFFRACTION100
3.709-27.63710.20741570.19051737X-RAY DIFFRACTION99
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)
11.4304-0.0936-1.80810.68110.81772.5366-0.1029-0.0587-0.1502-0.0092-0.06560.05140.0976-0.03520.20260.1155-0.0150.00110.10950.00570.107933.214330.992511.8525
2-0.0291-0.05970.17880.7716-0.97173.15140.0355-0.06720.03620.1218-0.1296-0.1135-0.28880.30240.17430.1373-0.0380.0060.17460.01090.201540.67635.81913.9832
30.8734-0.65040.34270.5461-0.44392.50550.11720.06040.11570.0132-0.0673-0.1655-0.18390.14850.01080.1876-0.05050.01370.10190.0080.197835.781545.213513.6167
41.99120.03111.39440.44240.32972.45460.1019-0.09640.06950.0748-0.0741-0.0020.0099-0.7596-0.02350.1499-0.008-0.01610.15270.00230.175127.735339.751913.471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 74 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 36 )
4X-RAY DIFFRACTION4chain 'B' and (resid 37 through 73 )

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