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- PDB-5hry: Computationally Designed Cyclic Dimer ank3C2_1 -

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Basic information

Entry
Database: PDB / ID: 5hry
TitleComputationally Designed Cyclic Dimer ank3C2_1
Componentsank3C2_1
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 Å
AuthorsCascio, D. / McNamara, D.E. / 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 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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

Downloads & links

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Assembly

Deposited unit
A: ank3C2_1
B: ank3C2_1
C: ank3C2_1
D: ank3C2_1
E: ank3C2_1
F: ank3C2_1
G: ank3C2_1
H: ank3C2_1


Theoretical massNumber of molelcules
Total (without water)144,1038
Polymers144,1038
Non-polymers00
Water57632
1
A: ank3C2_1
F: ank3C2_1


Theoretical massNumber of molelcules
Total (without water)36,0262
Polymers36,0262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-18 kcal/mol
Surface area12760 Å2
MethodPISA
2
B: ank3C2_1
E: ank3C2_1


Theoretical massNumber of molelcules
Total (without water)36,0262
Polymers36,0262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-15 kcal/mol
Surface area12310 Å2
MethodPISA
3
C: ank3C2_1
D: ank3C2_1


Theoretical massNumber of molelcules
Total (without water)36,0262
Polymers36,0262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-19 kcal/mol
Surface area12250 Å2
MethodPISA
4
G: ank3C2_1
H: ank3C2_1


Theoretical massNumber of molelcules
Total (without water)36,0262
Polymers36,0262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-16 kcal/mol
Surface area12370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.350, 106.180, 106.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ank3C2_1


Mass: 18012.885 Da / Num. of mol.: 8
Mutation: K49A, E50K, K53L, S57E, K82A, E83V, K86A, S90M, Q91H, K115E, K119I, S123A, Q124M, L153V, K156D, Q157H
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris pH 8.5, 200 mM MgCl2, 30% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→75.24 Å / Num. obs: 77138 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 34.06 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 11.63
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.073.70.4772.24195
2.05-2.110.4022.61196.6
2.11-2.170.3023.4195.3
2.17-2.230.2574.3197.1
2.23-2.310.2085.15196.4
2.31-2.390.1556.56196.9
2.39-2.480.1397.42195.8
2.48-2.580.1138.56196.3
2.58-2.690.1019.54194.9
2.69-2.830.09810.34192.9
2.83-2.980.07513.52194.8
2.98-3.160.06116.15194.3
3.16-3.380.05218.97193.3
3.38-3.650.04223.37191.4
3.65-40.03826.04186.7
4-4.470.03628.99190.1
4.47-5.160.03529.75189.2
5.16-6.320.03725.38188.4
6.32-8.940.02930.83183.2
8.940.02935.53180.8

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational model based on 4GMR

4gmr


Resolution: 2→75.24 Å / Cor.coef. Fo:Fc: 0.9377 / Cor.coef. Fo:Fc free: 0.9265 / SU R Cruickshank DPI: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.198 / SU Rfree Blow DPI: 0.163 / SU Rfree Cruickshank DPI: 0.169
RfactorNum. reflection% reflectionSelection details
Rfree0.2421 7706 10 %RANDOM
Rwork0.2164 ---
obs0.219 77065 93.88 %-
Displacement parametersBiso mean: 53.7 Å2
Baniso -1Baniso -2Baniso -3
1--10.9969 Å20 Å20 Å2
2--0.4606 Å20 Å2
3---10.5363 Å2
Refine analyzeLuzzati coordinate error obs: 0.372 Å
Refinement stepCycle: LAST / Resolution: 2→75.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8941 0 0 32 8973
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0099055HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1112279HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3209SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes314HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1311HARMONIC5
X-RAY DIFFRACTIONt_it9055HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.33
X-RAY DIFFRACTIONt_other_torsion17.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1157SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9792SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2693 565 10 %
Rwork0.2342 5085 -
all0.2378 5650 -
obs--93.88 %
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)
11.02950.29080.1992.63950.29761.6760.0826-0.06620.04480.4104-0.03520.40830.0253-0.1787-0.04740.36390.09910.0855-0.27860.0093-0.3291-24.7699-5.813212.5424
21.9618-0.41720.49311.70340.0941.28210.0609-0.06790.0204-0.10960.020.2039-0.0211-0.1495-0.08090.29580.0043-0.0179-0.16760.0296-0.2709-23.4296-51.3218-12.4084
31.08430.0180.22354.81840.92922.7621-0.01220.0798-0.0813-0.51660.058-0.187-0.21050.0154-0.04570.36490.0295-0.033-0.32010.0363-0.2439-2.459-15.8828-1.7997
41.1785-0.2284-0.04254.28670.81122.1833-0.0539-0.03470.18020.53930.1364-0.1953-0.02490.0821-0.08250.3802-0.0027-0.0237-0.32410.017-0.2349-1.2757-40.21572.8795
51.7897-0.6371-1.16182.44820.83913.198-0.0166-0.0842-0.04960.17040.08670.14610.0261-0.16-0.07010.23870.01130.0406-0.1550.0382-0.3031-21.218-54.69211.8875
61.32390.33060.71443.610.46782.95540.00040.00460.0457-0.3995-0.00190.1461-0.1467-0.07390.00160.31610.0946-0.03-0.22890.0192-0.3152-22.7203-1.4777-12.1092
71.95312.0134-0.38518.4807-1.85872.0344-0.0897-0.1132-0.2636-0.4703-0.2995-0.9640.2210.06730.38930.24850.06010.0924-0.33260.0461-0.18066.849212.4908-0.166
81.1536-0.90250.2995.5409-1.54762.8194-0.0634-0.06360.05480.1361-0.0614-0.7381-0.25590.07210.12480.2271-0.0162-0.0786-0.3135-0.0006-0.22577.536937.1631.2416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

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