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- PDB-5hrz: Computationally Designed Trimer 1na0C3_3 -

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Basic information

Entry
Database: PDB / ID: 5hrz
TitleComputationally Designed Trimer 1na0C3_3
ComponentsTPR domain protein 1na0C3_3
KeywordsDE NOVO PROTEIN / Protein Design / Designed Oligomeric Interface
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 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: TPR domain protein 1na0C3_3


Theoretical massNumber of molelcules
Total (without water)14,7051
Polymers14,7051
Non-polymers00
Water25214
1
A: TPR domain protein 1na0C3_3

A: TPR domain protein 1na0C3_3

A: TPR domain protein 1na0C3_3


Theoretical massNumber of molelcules
Total (without water)44,1163
Polymers44,1163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area3030 Å2
ΔGint-30 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.570, 83.570, 141.930
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
DetailsTrimer based on SEC-MALS and SAXS

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Components

#1: Protein TPR domain protein 1na0C3_3


Mass: 14705.200 Da / Num. of mol.: 1
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.: 14 / 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: 3.24 Å3/Da / Density % sol: 62.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4 M sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.15→64.48 Å / Num. obs: 10656 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 45.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 20.88
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.15-2.229.20.6753.3197.8
2.2-2.260.5664.711100
2.26-2.330.4475.69199.9
2.33-2.40.3856.541100
2.4-2.480.3287.781100
2.48-2.570.21910.421100
2.57-2.660.1911.981100
2.66-2.770.1614.731100
2.77-2.90.11519.211100
2.9-3.040.09422.511100
3.04-3.20.07426.61199.8
3.2-3.40.05931.471100
3.4-3.630.05138.571100
3.63-3.920.04642.79199.8
3.92-4.290.04145.13199.8
4.29-4.80.03844.43199.5
4.8-5.540.04145.14199.7
5.54-6.790.04145.21100
6.79-9.60.03447.211100

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational model based on 1NA0

1na0


Resolution: 2.15→64.48 Å / Cor.coef. Fo:Fc: 0.9562 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.146 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.135
RfactorNum. reflection% reflectionSelection details
Rfree0.206 946 8.89 %RANDOM
Rwork0.18 9694 --
obs0.1821 10640 99.92 %-
Displacement parametersBiso max: 115.81 Å2 / Biso mean: 48.28 Å2 / Biso min: 30.39 Å2
Baniso -1Baniso -2Baniso -3
1-3.185 Å20 Å20 Å2
2--3.185 Å20 Å2
3----6.3699 Å2
Refine analyzeLuzzati coordinate error obs: 0.256 Å
Refinement stepCycle: final / Resolution: 2.15→64.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 0 14 985
Biso mean---55.85 -
Num. residues----122
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d347SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes138HARMONIC5
X-RAY DIFFRACTIONt_it991HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion121SEMIHARMONIC5
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_contact1100SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d991HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1342HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion2.58
X-RAY DIFFRACTIONt_other_torsion19.27
LS refinement shellResolution: 2.15→2.4 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2048 279 9.38 %
Rwork0.1954 2696 -
all0.1963 2975 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: -3.4942 Å / Origin y: 26.6282 Å / Origin z: -11.8166 Å
111213212223313233
T-0.0256 Å2-0.021 Å20.0217 Å2--0.096 Å20.0263 Å2---0.0561 Å2
L0.6016 °20.366 °20.0488 °2-4.9959 °20.5258 °2--1.3914 °2
S-0.0082 Å °-0.0351 Å °-0.0088 Å °0.2147 Å °-0.0137 Å °0.093 Å °0.1884 Å °-0.0794 Å °0.022 Å °
Refinement TLS groupSelection details: { A|* }

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