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- PDB-22ly: De novo designed S-locus Protein 11 (SP11)-like protein (P212121 form) -

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Basic information

Entry
Database: PDB / ID: 22ly
TitleDe novo designed S-locus Protein 11 (SP11)-like protein (P212121 form)
ComponentsDe novo designed SP11-like protein
KeywordsDE NOVO PROTEIN / S-locus Protein 11 / pollen determinant
Function / homologyL(+)-TARTARIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMiyoshi, H. / Sakuma, K. / Moriwaki, Y. / Fushinobu, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24H02269 Japan
Japan Agency for Medical Research and Development (AMED)JP25ama121027 Japan
CitationJournal: Proteins / Year: 2026
Title: Structural and Stability Analysis of de Novo Designed Proteins Incorporating a Plant Self-Incompatibility Motif.
Authors: Miyoshi, H. / Sakuma, K. / Moriwaki, Y. / Aoyama, N. / Kashima, T. / Terada, T. / Miyanaga, A. / Fushinobu, S.
History
DepositionJan 16, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo designed SP11-like protein
C: De novo designed SP11-like protein
B: De novo designed SP11-like protein
D: De novo designed SP11-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1568
Polymers66,5564
Non-polymers6004
Water3,891216
1
A: De novo designed SP11-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7892
Polymers16,6391
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: De novo designed SP11-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7892
Polymers16,6391
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: De novo designed SP11-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7892
Polymers16,6391
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: De novo designed SP11-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7892
Polymers16,6391
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.234, 82.828, 118.210
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
De novo designed SP11-like protein


Mass: 16638.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.5M di-ammonium tartrate, 17.5% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2023
RadiationMonochromator: Double Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→48.16 Å / Num. obs: 46962 / % possible obs: 99.9 % / Redundancy: 27 % / Biso Wilson estimate: 27.69 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.19 / Net I/σ(I): 24.5
Reflection shellResolution: 2.09→2.22 Å / Mean I/σ(I) obs: 3.3 / Num. unique obs: 7418 / CC1/2: 0.918 / Rrim(I) all: 1.497 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48.16 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23925 2321 5 %RANDOM
Rwork0.20012 ---
obs0.20197 44357 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.905 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0 Å20 Å2
2--2.21 Å2-0 Å2
3----1.62 Å2
Refinement stepCycle: 1 / Resolution: 2.1→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4354 0 40 216 4610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124447
X-RAY DIFFRACTIONr_bond_other_d00.0164450
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.8736074
X-RAY DIFFRACTIONr_angle_other_deg0.5731.7510197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9085575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.054564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.48910709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025360
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02916
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.2885.4772315
X-RAY DIFFRACTIONr_mcbond_other5.2875.4772315
X-RAY DIFFRACTIONr_mcangle_it7.2669.8042885
X-RAY DIFFRACTIONr_mcangle_other7.2659.8042886
X-RAY DIFFRACTIONr_scbond_it6.7536.332132
X-RAY DIFFRACTIONr_scbond_other6.7536.3312131
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.93911.2533189
X-RAY DIFFRACTIONr_long_range_B_refined11.77660.044613
X-RAY DIFFRACTIONr_long_range_B_other11.79859.344574
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 141 -
Rwork0.259 3238 -
obs--100 %

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