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- PDB-9wm8: The crystal structure of AstaP-pink1 from a microalga -

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Basic information

Entry
Database: PDB / ID: 9wm8
TitleThe crystal structure of AstaP-pink1 from a microalga
ComponentsAstaP-pink1
KeywordsLIPID BINDING PROTEIN / FAS1 domain superfamily / carotenoprotein / astaxanthin / coloration / bathochromic shift
Function / homologyASTAXANTHIN
Function and homology information
Biological speciesScenedesmaceae sp. (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsShomura, Y. / Kawasaki, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP25ama121001 Japan
Japan Society for the Promotion of Science (JSPS)JP24H02093 Japan
CitationJournal: J.Struct.Biol. / Year: 2026
Title: Structural basis for spectral red shift and UVA absorption in the microalgal water-soluble astaxanthin-binding protein AstaP-pink1.
Authors: Mitsui, T. / Shomura, Y. / Furubayashi, M. / Kato, R. / Takaichi, S. / Kawasaki, S.
History
DepositionSep 3, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AstaP-pink1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5552
Polymers19,9581
Non-polymers5971
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-12 kcal/mol
Surface area8600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.845, 52.629, 71.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein AstaP-pink1


Mass: 19957.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GenBank:BBN91623.1 / Source: (gene. exp.) Scenedesmaceae sp. (plant) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-AXT / ASTAXANTHIN / 3,3'-DIHYDROXY-BETA,BETA-CAROTENE-4,4'-DIONE


Mass: 596.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H52O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.97 Å3/Da / Density % sol: 37.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl, 20% (v/v) PEG300, 5% (w/v) PEG8000, and 10% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.018 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.018 Å / Relative weight: 1
ReflectionResolution: 1.7→71.37 Å / Num. obs: 17985 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 21.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Net I/σ(I): 13.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 918 / CC1/2: 0.823 / Rpim(I) all: 0.309 / Rrim(I) all: 0.721 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.7→42.36 Å / SU ML: 0.2001 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6643
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2202 923 5.15 %
Rwork0.1802 17003 -
obs0.1822 17926 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.49 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1197 0 44 101 1342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01591365
X-RAY DIFFRACTIONf_angle_d1.37541869
X-RAY DIFFRACTIONf_chiral_restr0.1225
X-RAY DIFFRACTIONf_plane_restr0.0115252
X-RAY DIFFRACTIONf_dihedral_angle_d14.6397518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.790.30391400.22662362X-RAY DIFFRACTION99.72
1.79-1.90.21271280.18582403X-RAY DIFFRACTION99.96
1.9-2.050.22071230.15892373X-RAY DIFFRACTION99.96
2.05-2.250.2151390.15652403X-RAY DIFFRACTION99.96
2.25-2.580.16911250.16452437X-RAY DIFFRACTION99.96
2.58-3.250.20911190.18452465X-RAY DIFFRACTION99.96
3.25-42.360.23661490.18792560X-RAY DIFFRACTION99.89
Refinement TLS params.Method: refined / Origin x: -7.74867908539 Å / Origin y: -8.27543129227 Å / Origin z: 13.5788639851 Å
111213212223313233
T0.152225938333 Å20.00169541941247 Å2-0.0180226124498 Å2-0.158445797142 Å2-0.0127033531436 Å2--0.146166116285 Å2
L1.17606306731 °2-0.0929972278945 °20.193768663839 °2-1.62132602424 °2-0.0578413860163 °2--1.10514005841 °2
S0.0300295474187 Å °0.00965020973031 Å °0.0291695276416 Å °0.0311467898141 Å °-0.0720458754286 Å °0.0124310551957 Å °-0.0206078944997 Å °-0.150728593595 Å °-0.000296997050734 Å °
Refinement TLS groupSelection details: all

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