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- PDB-22iy: Crystal structure of the unliganded microalgal AstaP-pink1 carote... -

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Basic information

Entry
Database: PDB / ID: 22iy
TitleCrystal structure of the unliganded microalgal AstaP-pink1 carotenoprotein
ComponentsAstaxanthin-binding pink protein of fasciclin family
KeywordsTRANSPORT PROTEIN / Microalgal protein / carotenoprotein / AstaP-pink1 / unliganded form / astaxanthin-binding pink protein
Function / homology: / Fasciclin domain / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts. / FAS1 domain / FAS1 domain superfamily / FAS1/BIgH3 domain profile. / extracellular space / Astaxanthin-binding pink protein of fasciclin family
Function and homology information
Biological speciesScenedesmus sp. Oki-4N (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSluchanko, N.N. / Slonimskiy, Y.B. / Varfolomeeva, L.A. / Popov, V.O. / Boyko, K.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation Russian Federation
CitationJournal: To Be Published
Title: Crystal structure of the unliganded microalgal AstaP-pink1 carotenoprotein
Authors: Sluchanko, N.N. / Slonimskiy, Y.B. / Varfolomeeva, L.A. / Popov, V.O. / Boyko, K.M.
History
DepositionJan 13, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Astaxanthin-binding pink protein of fasciclin family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2792
Polymers20,1871
Non-polymers921
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint1 kcal/mol
Surface area7980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.483, 56.525, 58.692
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 Astaxanthin-binding pink protein of fasciclin family / Microalgal AstaP-pink1 carotenoprotein


Mass: 20186.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scenedesmus sp. Oki-4N (plant) / Gene: astaP-pn1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7G1GF05
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 1.66 Å3/Da / Density % sol: 26.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris pH 8.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.9772 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 1.65→40.71 Å / Num. obs: 16831 / % possible obs: 100 % / Redundancy: 10.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.062 / Rrim(I) all: 0.203 / Χ2: 1.01 / Net I/σ(I): 8.8 / Num. measured all: 176663
Reflection shellResolution: 1.65→1.68 Å / % possible obs: 100 % / Redundancy: 10.4 % / Rmerge(I) obs: 3.096 / Num. measured all: 8527 / Num. unique obs: 821 / CC1/2: 0.416 / Rpim(I) all: 0.996 / Rrim(I) all: 3.256 / Χ2: 1.01 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→40.71 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.951 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22806 839 5 %RANDOM
Rwork0.17568 ---
obs0.17827 15946 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: 26.331 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å2-0 Å2-0 Å2
2---0.12 Å20 Å2
3---1 Å2
Refinement stepCycle: 1 / Resolution: 1.65→40.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 0 6 119 1294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121216
X-RAY DIFFRACTIONr_bond_other_d0.0050.0161201
X-RAY DIFFRACTIONr_angle_refined_deg2.2161.7961659
X-RAY DIFFRACTIONr_angle_other_deg1.1961.772765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6385164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.00558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80310203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1790.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021448
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02242
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_it1.9761.479647
X-RAY DIFFRACTIONr_mcbond_other1.9711.479647
X-RAY DIFFRACTIONr_mcangle_it2.9952.649808
X-RAY DIFFRACTIONr_mcangle_other2.9952.657809
X-RAY DIFFRACTIONr_scbond_it3.0981.727569
X-RAY DIFFRACTIONr_scbond_other3.0981.732570
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6113.029850
X-RAY DIFFRACTIONr_long_range_B_refined6.69923.11313
X-RAY DIFFRACTIONr_long_range_B_other6.66817.891274
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 45 -
Rwork0.325 1193 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 5.1084 Å / Origin y: 8.2697 Å / Origin z: 11.5982 Å
111213212223313233
T0.0287 Å20.0058 Å2-0.0029 Å2-0.0084 Å20.0138 Å2--0.0478 Å2
L2.4502 °2-0.7322 °20.3903 °2-2.3836 °2-0.5891 °2--1.9583 °2
S-0.0405 Å °-0.1163 Å °-0.1108 Å °0.2091 Å °0.0309 Å °-0.0726 Å °0.0813 Å °0.0265 Å °0.0097 Å °

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