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- PDB-22lx: De novo designed S-locus Protein 11 (SP11)-like protein (P6522 form) -

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Basic information

Entry
Database: PDB / ID: 22lx
TitleDe novo designed S-locus Protein 11 (SP11)-like protein (P6522 form)
ComponentsDe novo designed SP11-like protein
KeywordsDE NOVO PROTEIN / S-locus Protein 11 / pollen determinant
Function / homologyACETATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0096
Polymers16,6391
Non-polymers3705
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-15 kcal/mol
Surface area8000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.300, 64.300, 126.221
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-203-

SO4

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Components

#1: Protein De novo designed SP11-like protein


Mass: 16638.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: 0.16M ammonium sulfate, 0.08M Na-acetate (pH 4.4), 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 20, 2023
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→51 Å / Num. obs: 25451 / % possible obs: 99.6 % / Redundancy: 16.8 % / Biso Wilson estimate: 16.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.015 / Rrim(I) all: 0.063 / Net I/σ(I): 25.1
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.965 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1140 / CC1/2: 0.609 / Rpim(I) all: 0.399 / Rrim(I) all: 1.05

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→51 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21339 1263 5 %RANDOM
Rwork0.17951 ---
obs0.18119 24122 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.563 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.12 Å2-0 Å2
2---0.25 Å20 Å2
3---0.8 Å2
Refinement stepCycle: 1 / Resolution: 1.5→51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1101 0 20 99 1220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121184
X-RAY DIFFRACTIONr_bond_other_d00.0161179
X-RAY DIFFRACTIONr_angle_refined_deg2.1811.871621
X-RAY DIFFRACTIONr_angle_other_deg0.7841.752699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8395155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.618518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30510190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021436
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02252
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_it1.9942.037612
X-RAY DIFFRACTIONr_mcbond_other1.9162.031611
X-RAY DIFFRACTIONr_mcangle_it2.6063.64766
X-RAY DIFFRACTIONr_mcangle_other2.6053.641767
X-RAY DIFFRACTIONr_scbond_it4.1982.668572
X-RAY DIFFRACTIONr_scbond_other4.1922.652559
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3934.573834
X-RAY DIFFRACTIONr_long_range_B_refined7.56523.731285
X-RAY DIFFRACTIONr_long_range_B_other7.51222.591254
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 66 -
Rwork0.283 1666 -
obs--94.75 %

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