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- PDB-5j73: De novo design of protein homo-oligomers with modular hydrogen bo... -

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Basic information

Entry
Database: PDB / ID: 5j73
TitleDe novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity
Componentsprotein design 2L4HC2_9
KeywordsDE NOVO PROTEIN / rosetta / de novo design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 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
DepositionApr 5, 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
A: protein design 2L4HC2_9
B: protein design 2L4HC2_9
C: protein design 2L4HC2_9
D: protein design 2L4HC2_9


Theoretical massNumber of molelcules
Total (without water)37,9114
Polymers37,9114
Non-polymers00
Water28816
1
A: protein design 2L4HC2_9
B: protein design 2L4HC2_9


Theoretical massNumber of molelcules
Total (without water)18,9552
Polymers18,9552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-29 kcal/mol
Surface area9580 Å2
MethodPISA
2
C: protein design 2L4HC2_9
D: protein design 2L4HC2_9


Theoretical massNumber of molelcules
Total (without water)18,9552
Polymers18,9552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-29 kcal/mol
Surface area9370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.790, 91.970, 45.840
Angle α, β, γ (deg.)90.00, 111.14, 90.00
Int Tables number4
Space group name H-MP1211
DetailsDimer according to SAXS

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Components

#1: Protein
protein design 2L4HC2_9


Mass: 9477.684 Da / Num. of mol.: 4
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.: 16 / 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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium citrate tribasic dehydrate pH 5.0, 30 % PEG MME 550

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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: 2.56→38.77 Å / Num. obs: 9454 / % possible obs: 99.83 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 17.1

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Processing

Software
NameVersionClassification
PHENIXdev_1616refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→38.77 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 26.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 944 9.99 %
Rwork0.2069 --
obs0.2117 9449 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→38.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2471 0 0 16 2487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052471
X-RAY DIFFRACTIONf_angle_d0.8383290
X-RAY DIFFRACTIONf_dihedral_angle_d16.1511042
X-RAY DIFFRACTIONf_chiral_restr0.033380
X-RAY DIFFRACTIONf_plane_restr0.003435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5602-2.69520.37041290.2831233X-RAY DIFFRACTION100
2.6952-2.8640.27161410.24951201X-RAY DIFFRACTION100
2.864-3.08510.3381310.25841199X-RAY DIFFRACTION100
3.0851-3.39540.28841410.2341215X-RAY DIFFRACTION100
3.3954-3.88630.25271330.20391205X-RAY DIFFRACTION100
3.8863-4.89480.23031310.17941227X-RAY DIFFRACTION100
4.8948-38.77480.20881380.1791225X-RAY DIFFRACTION99

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