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- PDB-5hs0: Computationally Designed Cyclic Tetramer ank1C4_7 -

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Basic information

Entry
Database: PDB / ID: 5hs0
TitleComputationally Designed Cyclic Tetramer ank1C4_7
ComponentsAnkyrin domain protein ank1C4_7
KeywordsDE NOVO PROTEIN / Protein Design / Designed Oligomeric Interface
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMcNamara, D.E. / Cascio, D. / Fallas, J.A. / Baker, D. / Yeates, T.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1332907 United States
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
DepositionJan 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Ankyrin domain protein ank1C4_7
B: Ankyrin domain protein ank1C4_7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,72911
Polymers35,8762
Non-polymers8539
Water34219
1
A: Ankyrin domain protein ank1C4_7
B: Ankyrin domain protein ank1C4_7
hetero molecules

A: Ankyrin domain protein ank1C4_7
B: Ankyrin domain protein ank1C4_7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,45822
Polymers71,7524
Non-polymers1,70518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area7330 Å2
ΔGint-181 kcal/mol
Surface area26320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.450, 110.450, 182.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
DetailsTetramer based on SEC-MALS and SAXS

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Components

#1: Protein Ankyrin domain protein ank1C4_7


Mass: 17938.111 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21 NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 4.49 Å3/Da / Density % sol: 72.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100 mM Sodium Acetate pH 4.6, 2.0 M AmSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→84.75 Å / Num. obs: 26424 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Biso Wilson estimate: 54.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Net I/σ(I): 17.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.4-2.47100.67731100
2.46-2.530.5624.171100
2.53-2.60.4335.36199.8
2.6-2.680.3426.621100
2.68-2.770.3057.29199.5
2.77-2.870.2529.021100
2.87-2.980.20511.181100
2.98-3.10.1613.791100
3.1-3.240.13415.961100
3.24-3.390.10619.37199.8
3.39-3.580.08125.071100
3.58-3.790.07128.041100
3.79-4.060.06629.66199.6
4.06-4.380.0629.87199.5
4.38-4.80.05532.78199.8
4.8-5.370.05533.231100
5.37-6.20.05431.05199.9
6.2-7.590.04733.25199.5
7.59-10.730.03836.16199

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational model based on 4GPM

4gpm


Resolution: 2.4→84.75 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.92
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 2643 10 %RANDOM
Rwork0.1796 23780 --
obs0.1825 26423 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.94 Å2 / Biso mean: 66.5002 Å2 / Biso min: 37.45 Å2
Refinement stepCycle: final / Resolution: 2.4→84.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 48 19 2446
Biso mean--93.11 54.46 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042444
X-RAY DIFFRACTIONf_angle_d0.7623304
X-RAY DIFFRACTIONf_chiral_restr0.022387
X-RAY DIFFRACTIONf_plane_restr0.006435
X-RAY DIFFRACTIONf_dihedral_angle_d12.964899
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.44370.26541340.238112071341100
2.4437-2.49070.24291360.218712241360100
2.4907-2.54150.24961370.212612301367100
2.5415-2.59680.24771350.193112161351100
2.5968-2.65720.2531370.195512331370100
2.6572-2.72360.24731360.19612211357100
2.7236-2.79730.27941350.210212201355100
2.7973-2.87960.27031380.217612341372100
2.8796-2.97250.26951390.236912521391100
2.9725-3.07880.24871380.21812471385100
3.0788-3.20210.23721360.229712271363100
3.2021-3.34780.30921400.21412601400100
3.3478-3.52430.21771380.196312361374100
3.5243-3.74510.21011400.174412581398100
3.7451-4.03430.18061390.163212551394100
4.0343-4.44020.18571410.154412691410100
4.4402-5.08270.16931430.146812841427100
5.0827-6.40330.20561450.191813111456100
6.4033-84.80490.161560.14671396155299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0917-0.4068-2.61891.29140.61733.840.02420.29010.1685-0.10750.0446-0.1823-0.1167-0.3195-0.05810.3639-0.03930.01010.38330.0010.4508-15.2573-34.8083.1179
22.1956-0.1296-0.16164.0273-0.47463.32110.0680.4487-0.1599-0.5199-0.0087-0.02840.420.1595-0.03790.46360.0503-0.07190.5742-0.10290.4796-36.2487-57.5875-6.7746
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 160 )A1 - 160
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 158 )B1 - 158

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