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- PDB-6g6n: Crystal structure of the computationally designed Tako8 protein in C2 -

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Basic information

Entry
Database: PDB / ID: 6g6n
TitleCrystal structure of the computationally designed Tako8 protein in C2
ComponentsTako8
KeywordsDE NOVO PROTEIN / Artificial protein / WD40 proteins
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsNoguchi, H. / Addy, C. / Simoncini, D. / Van Meervelt, L. / Schiex, T. / Zhang, K.Y.J. / Tame, J.R.H. / Voet, A.R.D.
Funding support Belgium, Japan, 2items
OrganizationGrant numberCountry
G0E4717N, G0F9316N, G051917N Belgium
Japan Science and Technology16H04779 Japan
CitationJournal: IUCrJ / Year: 2019
Title: Computational design of symmetrical eight-bladed beta-propeller proteins.
Authors: Noguchi, H. / Addy, C. / Simoncini, D. / Wouters, S. / Mylemans, B. / Van Meervelt, L. / Schiex, T. / Zhang, K.Y.J. / Tame, J.R.H. / Voet, A.R.D.
History
DepositionApr 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 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

Downloads & links

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Assembly

Deposited unit
A: Tako8
B: Tako8
C: Tako8


Theoretical massNumber of molelcules
Total (without water)105,0733
Polymers105,0733
Non-polymers00
Water3,927218
1
A: Tako8


Theoretical massNumber of molelcules
Total (without water)35,0241
Polymers35,0241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tako8


Theoretical massNumber of molelcules
Total (without water)35,0241
Polymers35,0241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tako8


Theoretical massNumber of molelcules
Total (without water)35,0241
Polymers35,0241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.548, 132.297, 81.015
Angle α, β, γ (deg.)90.00, 125.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tako8


Mass: 35024.230 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.: 218 / 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: 1.95 Å3/Da / Density % sol: 36.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: 0.1M citrate pH5.0, 3.4M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→46.774 Å / Num. obs: 54194 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rpim(I) all: 0.025 / Net I/σ(I): 18.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3.6 / CC1/2: 0.862 / Rpim(I) all: 0.304 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.001→46.774 Å / Cross valid method: FREE R-VALUE / σ(F): 41.37 / Phase error: 43.12
RfactorNum. reflection% reflection
Rfree0.2663 2489 4.59 %
Rwork0.2426 --
obs0.2459 54194 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.001→46.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7257 0 0 218 7475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037350
X-RAY DIFFRACTIONf_angle_d0.629993
X-RAY DIFFRACTIONf_dihedral_angle_d6.2734341
X-RAY DIFFRACTIONf_chiral_restr0.051216
X-RAY DIFFRACTIONf_plane_restr0.0021286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0008-2.03930.38431860.39682961X-RAY DIFFRACTION94
2.0393-2.08090.42121120.41872905X-RAY DIFFRACTION96
2.0809-2.12610.36871220.40942849X-RAY DIFFRACTION96
2.1261-2.17550.46171130.42142911X-RAY DIFFRACTION96
2.1755-2.22990.46541130.42792830X-RAY DIFFRACTION96
2.2299-2.29010.4451990.38062912X-RAY DIFFRACTION97
2.2901-2.35740.44591400.40862756X-RAY DIFFRACTION95
2.3574-2.43340.40971420.40972958X-RAY DIFFRACTION95
2.4334-2.52030.42211480.38442864X-RAY DIFFRACTION95
2.5203-2.6210.37841420.34162871X-RAY DIFFRACTION95
2.621-2.74010.31261190.33832860X-RAY DIFFRACTION96
2.7401-2.88430.33541150.30982849X-RAY DIFFRACTION96
2.8843-3.06450.31841160.32072898X-RAY DIFFRACTION96
3.0645-3.30040.32051770.26022857X-RAY DIFFRACTION94
3.3004-3.63120.25591830.21682800X-RAY DIFFRACTION94
3.6312-4.15360.24141700.18222792X-RAY DIFFRACTION94
4.1536-5.22160.17041530.14952901X-RAY DIFFRACTION94
5.2216-22.05080.17831350.18012902X-RAY DIFFRACTION95

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