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- PDB-5j0j: De novo design of protein homo-oligomers with modular hydrogen bo... -

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Basic information

Entry
Database: PDB / ID: 5j0j
TitleDe novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity
Componentsdesigned protein 2L6HC3_6
KeywordsDE NOVO PROTEIN / rosetta / de novo design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.256 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 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: designed protein 2L6HC3_6
B: designed protein 2L6HC3_6
C: designed protein 2L6HC3_6


Theoretical massNumber of molelcules
Total (without water)27,4913
Polymers27,4913
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-55 kcal/mol
Surface area11290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.010, 34.386, 61.542
Angle α, β, γ (deg.)90.00, 92.40, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTrimer according to

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Components

#1: Protein designed protein 2L6HC3_6


Mass: 9163.594 Da / Num. of mol.: 3
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.: 39 / 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: 1.92 Å3/Da / Density % sol: 36.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium Fluoride, 0.1 M MES pH 5.5 , 20 % PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.256→49.97 Å / Num. obs: 9728 / % possible obs: 96.32 % / Redundancy: 4.1 % / Net I/σ(I): 20

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Processing

Software
NameVersionClassification
PHENIXdev_1616refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.256→49.966 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 28.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2751 970 9.97 %
Rwork0.2269 --
obs0.2318 9727 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.256→49.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1729 0 0 39 1768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081732
X-RAY DIFFRACTIONf_angle_d0.7992309
X-RAY DIFFRACTIONf_dihedral_angle_d18.505729
X-RAY DIFFRACTIONf_chiral_restr0.039280
X-RAY DIFFRACTIONf_plane_restr0.003291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2559-2.37480.32431200.27381022X-RAY DIFFRACTION82
2.3748-2.52360.30491390.23441284X-RAY DIFFRACTION99
2.5236-2.71840.24521450.24631286X-RAY DIFFRACTION100
2.7184-2.9920.27711380.23421278X-RAY DIFFRACTION100
2.992-3.42480.27961410.22981315X-RAY DIFFRACTION100
3.4248-4.31450.2461470.19071305X-RAY DIFFRACTION100
4.3145-49.97840.29631400.24221267X-RAY DIFFRACTION94

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