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- PDB-5k7v: Computational Design of Self-Assembling Cyclic Protein Homooligomers -

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Basic information

Entry
Database: PDB / ID: 5k7v
TitleComputational Design of Self-Assembling Cyclic Protein Homooligomers
ComponentsDesigned protein HR00C3
KeywordsDE NOVO PROTEIN / rosetta / de novo design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.165 Å
AuthorsSankaran, B. / Zwart, P.H. / Fallas, J.A. / Pereira, J.H. / Ueda, G. / Baker, D.
CitationJournal: Nat Chem / Year: 2017
Title: Computational design of self-assembling cyclic protein homo-oligomers.
Authors: Fallas, J.A. / Ueda, G. / Sheffler, W. / Nguyen, V. / McNamara, D.E. / Sankaran, B. / Pereira, J.H. / Parmeggiani, F. / Brunette, T.J. / Cascio, D. / Yeates, T.R. / Zwart, P. / Baker, D.
History
DepositionMay 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Designed protein HR00C3
B: Designed protein HR00C3
C: Designed protein HR00C3


Theoretical massNumber of molelcules
Total (without water)94,3273
Polymers94,3273
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-28 kcal/mol
Surface area35790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.005, 159.005, 94.982
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
DetailsTrimer according to SAXS

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Components

#1: Protein Designed protein HR00C3


Mass: 31442.357 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.: 43 / 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: 3.67 Å3/Da / Density % sol: 66.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.3 M Sodium Citrate, 0.1 M Hepes pH 7.5 and 15 % 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: Sep 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.16→46 Å / Num. obs: 23543 / % possible obs: 98 % / Redundancy: 9.8 % / Net I/σ(I): 13

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Processing

Software
NameVersionClassification
PHENIXdev_1616refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementResolution: 3.165→46 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.67
RfactorNum. reflection% reflection
Rfree0.223 2006 8.52 %
Rwork0.2011 --
obs0.2129 23543 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.165→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6354 0 0 43 6397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036399
X-RAY DIFFRACTIONf_angle_d0.7028634
X-RAY DIFFRACTIONf_dihedral_angle_d12.7052388
X-RAY DIFFRACTIONf_chiral_restr0.0291089
X-RAY DIFFRACTIONf_plane_restr0.0021086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1672-3.24640.49891120.35831234X-RAY DIFFRACTION73
3.2464-3.33410.28041390.26351525X-RAY DIFFRACTION92
3.3341-3.43220.27791500.251548X-RAY DIFFRACTION91
3.4322-3.5430.32781410.24511545X-RAY DIFFRACTION92
3.543-3.66950.27341400.26121526X-RAY DIFFRACTION92
3.6695-3.81640.27761480.2361556X-RAY DIFFRACTION91
3.8164-3.990.2281410.22781568X-RAY DIFFRACTION92
3.99-4.20020.22941440.19381542X-RAY DIFFRACTION91
4.2002-4.46320.19491410.19021545X-RAY DIFFRACTION92
4.4632-4.80740.20621460.19071570X-RAY DIFFRACTION91
4.8074-5.29060.22921430.20841578X-RAY DIFFRACTION92
5.2906-6.05470.3271440.25211555X-RAY DIFFRACTION92
6.0547-7.62260.2351490.20741590X-RAY DIFFRACTION91
7.6226-45.90560.15121560.14631659X-RAY DIFFRACTION91

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