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- PDB-5j0l: De novo design of protein homo-oligomers with modular hydrogen bo... -

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Basic information

Entry
Database: PDB / ID: 5j0l
TitleDe novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity
Componentsdesigned protein 3L6HC2_2
KeywordsDE NOVO PROTEIN / rosetta / de novo design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 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 1.0Jul 6, 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 / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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 3L6HC2_2
B: designed protein 3L6HC2_2
C: designed protein 3L6HC2_2
D: designed protein 3L6HC2_2
E: designed protein 3L6HC2_2
F: designed protein 3L6HC2_2


Theoretical massNumber of molelcules
Total (without water)95,8206
Polymers95,8206
Non-polymers00
Water2,360131
1
A: designed protein 3L6HC2_2
B: designed protein 3L6HC2_2


Theoretical massNumber of molelcules
Total (without water)31,9402
Polymers31,9402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-27 kcal/mol
Surface area13230 Å2
MethodPISA
2
C: designed protein 3L6HC2_2
D: designed protein 3L6HC2_2


Theoretical massNumber of molelcules
Total (without water)31,9402
Polymers31,9402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-31 kcal/mol
Surface area12740 Å2
MethodPISA
3
E: designed protein 3L6HC2_2
F: designed protein 3L6HC2_2


Theoretical massNumber of molelcules
Total (without water)31,9402
Polymers31,9402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-26 kcal/mol
Surface area12520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.650, 152.650, 70.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
designed protein 3L6HC2_2


Mass: 15969.917 Da / Num. of mol.: 6
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.: 131 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium Acetate trihydrate pH 4.5, 3.0 M Sodium chloride

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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: Jan 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.63→66.1 Å / Num. obs: 27911 / % possible obs: 99.97 % / Redundancy: 12.5 % / Net I/σ(I): 17.9

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Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→66.099 Å / SU ML: 0.78 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 30.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2883 2002 7.17 %
Rwork0.2321 --
obs0.2362 27909 99.96 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.217 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.9336 Å2-0 Å20 Å2
2---1.9336 Å2-0 Å2
3---3.8672 Å2
Refinement stepCycle: LAST / Resolution: 2.63→66.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5566 0 0 131 5697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055559
X-RAY DIFFRACTIONf_angle_d0.7367379
X-RAY DIFFRACTIONf_dihedral_angle_d15.7162291
X-RAY DIFFRACTIONf_chiral_restr0.054841
X-RAY DIFFRACTIONf_plane_restr0.002980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6302-2.69590.47471400.32411827X-RAY DIFFRACTION100
2.6959-2.76880.41331390.30111834X-RAY DIFFRACTION100
2.7688-2.85030.37071430.27341842X-RAY DIFFRACTION100
2.8503-2.94230.32741440.27691836X-RAY DIFFRACTION100
2.9423-3.04750.3371440.251842X-RAY DIFFRACTION100
3.0475-3.16950.32131410.24871841X-RAY DIFFRACTION100
3.1695-3.31370.31161410.23171824X-RAY DIFFRACTION100
3.3137-3.48840.29471460.22071857X-RAY DIFFRACTION100
3.4884-3.7070.24621430.20221854X-RAY DIFFRACTION100
3.707-3.99310.28111380.21391851X-RAY DIFFRACTION100
3.9931-4.39490.25911440.19481855X-RAY DIFFRACTION100
4.3949-5.03070.24811410.21621848X-RAY DIFFRACTION100
5.0307-6.33730.32891490.29641879X-RAY DIFFRACTION100
6.3373-66.12020.22561490.20751917X-RAY DIFFRACTION100

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