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- PDB-5j0i: De novo design of protein homo-oligomers with modular hydrogen bo... -

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Basic information

Entry
Database: PDB / ID: 5j0i
TitleDe novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity
ComponentsDesigned protein 2L6HC3_12
KeywordsDE NOVO PROTEIN / rosetta / de novo design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 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 1.1Jul 20, 2016Group: Data collection
Revision 1.2Nov 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 1.3Mar 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: Designed protein 2L6HC3_12


Theoretical massNumber of molelcules
Total (without water)9,1841
Polymers9,1841
Non-polymers00
Water37821
1
A: Designed protein 2L6HC3_12

A: Designed protein 2L6HC3_12

A: Designed protein 2L6HC3_12


Theoretical massNumber of molelcules
Total (without water)27,5513
Polymers27,5513
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area5960 Å2
ΔGint-57 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.158, 44.158, 153.326
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsTrimer according to gel filtration, SEC-MALS

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Components

#1: Protein Designed protein 2L6HC3_12


Mass: 9183.677 Da / Num. of mol.: 1
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.: 21 / 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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.2 M Sodium Malonate pH 5.0

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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: Sep 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→38.33 Å / Num. obs: 4361 / % possible obs: 86.72 % / Redundancy: 18.3 % / Net I/σ(I): 14.32

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Processing

Software
NameVersionClassification
PHENIXdev_1616refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.202→38.33 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2547 435 10.02 %
Rwork0.2249 --
obs0.2279 4340 86.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.202→38.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms596 0 0 21 617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.025621
X-RAY DIFFRACTIONf_angle_d1.988833
X-RAY DIFFRACTIONf_dihedral_angle_d20.469261
X-RAY DIFFRACTIONf_chiral_restr0.134101
X-RAY DIFFRACTIONf_plane_restr0.01107
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2015-2.520.3431930.2923834X-RAY DIFFRACTION58
2.52-3.17470.28851630.23921468X-RAY DIFFRACTION99
3.1747-38.33730.22741790.20781603X-RAY DIFFRACTION100

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