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- PDB-6g6q: Crystal structure of the computationally designed Ika4 protein -

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Basic information

Entry
Database: PDB / ID: 6g6q
TitleCrystal structure of the computationally designed Ika4 protein
ComponentsIka4
KeywordsDE NOVO PROTEIN / Artificial protein / WD40 proteins
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
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 / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
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: Ika4
B: Ika4
C: Ika4
D: Ika4
E: Ika4
F: Ika4
G: Ika4
H: Ika4
I: Ika4
J: Ika4
K: Ika4
L: Ika4


Theoretical massNumber of molelcules
Total (without water)209,11812
Polymers209,11812
Non-polymers00
Water7,764431
1
A: Ika4
B: Ika4


Theoretical massNumber of molelcules
Total (without water)34,8532
Polymers34,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-25 kcal/mol
Surface area13100 Å2
MethodPISA
2
C: Ika4
D: Ika4


Theoretical massNumber of molelcules
Total (without water)34,8532
Polymers34,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-25 kcal/mol
Surface area13310 Å2
MethodPISA
3
E: Ika4
F: Ika4


Theoretical massNumber of molelcules
Total (without water)34,8532
Polymers34,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-23 kcal/mol
Surface area12660 Å2
MethodPISA
4
G: Ika4
H: Ika4


Theoretical massNumber of molelcules
Total (without water)34,8532
Polymers34,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-29 kcal/mol
Surface area13670 Å2
MethodPISA
5
I: Ika4
J: Ika4


Theoretical massNumber of molelcules
Total (without water)34,8532
Polymers34,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-27 kcal/mol
Surface area13470 Å2
MethodPISA
6
K: Ika4
L: Ika4


Theoretical massNumber of molelcules
Total (without water)34,8532
Polymers34,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-23 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.520, 219.190, 264.910
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
Ika4


Mass: 17426.537 Da / Num. of mol.: 12
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.: 431 / 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: 3.72 Å3/Da / Density % sol: 66.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES pH7.5, 0.2M sodium acetate, 25% (w/v) PEG3350

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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: 2.5→49.07 Å / Num. obs: 109112 / % possible obs: 99.7 % / Redundancy: 9 % / CC1/2: 0.997 / Rpim(I) all: 0.046 / Net I/σ(I): 11.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 2.7 / CC1/2: 0.841 / Rpim(I) all: 0.277 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→49.069 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.3
RfactorNum. reflection% reflection
Rfree0.2287 5330 4.89 %
Rwork0.1921 --
obs0.1939 108904 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→49.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14272 0 0 431 14703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214502
X-RAY DIFFRACTIONf_angle_d0.50919686
X-RAY DIFFRACTIONf_dihedral_angle_d4.2848360
X-RAY DIFFRACTIONf_chiral_restr0.0512353
X-RAY DIFFRACTIONf_plane_restr0.0022481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.52840.3091690.2513473X-RAY DIFFRACTION100
2.5284-2.55820.31941700.24233436X-RAY DIFFRACTION100
2.5582-2.58940.30331650.23223351X-RAY DIFFRACTION100
2.5894-2.62210.27041710.24333446X-RAY DIFFRACTION100
2.6221-2.65660.32641750.24783446X-RAY DIFFRACTION100
2.6566-2.6930.28381970.22983407X-RAY DIFFRACTION100
2.693-2.73150.30691860.23373343X-RAY DIFFRACTION100
2.7315-2.77230.28521660.23863466X-RAY DIFFRACTION100
2.7723-2.81560.29271750.23943492X-RAY DIFFRACTION100
2.8156-2.86170.27861600.22613364X-RAY DIFFRACTION100
2.8617-2.91110.28161940.22673400X-RAY DIFFRACTION100
2.9111-2.9640.28241680.22843502X-RAY DIFFRACTION100
2.964-3.0210.25111900.23153349X-RAY DIFFRACTION100
3.021-3.08270.30861750.24263441X-RAY DIFFRACTION100
3.0827-3.14970.28351800.22713473X-RAY DIFFRACTION100
3.1497-3.22290.25331640.21473412X-RAY DIFFRACTION100
3.2229-3.30350.27831610.21113461X-RAY DIFFRACTION100
3.3035-3.39280.26281700.20553471X-RAY DIFFRACTION100
3.3928-3.49260.24862100.19613390X-RAY DIFFRACTION100
3.4926-3.60530.23861780.1853471X-RAY DIFFRACTION100
3.6053-3.73410.21851970.18753417X-RAY DIFFRACTION100
3.7341-3.88360.20041630.17913482X-RAY DIFFRACTION100
3.8836-4.06020.18581900.17663443X-RAY DIFFRACTION99
4.0602-4.27420.20061600.15533449X-RAY DIFFRACTION99
4.2742-4.54180.17861860.14553474X-RAY DIFFRACTION99
4.5418-4.89220.16871850.14273477X-RAY DIFFRACTION99
4.8922-5.3840.17831650.15723506X-RAY DIFFRACTION99
5.384-6.16170.20461760.18143487X-RAY DIFFRACTION99
6.1617-7.75820.21351980.19933550X-RAY DIFFRACTION98
7.7582-49.07850.17191860.17723695X-RAY DIFFRACTION98

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