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- PDB-9kue: Crystal structure of the soluble green pigment protein from Tetti... -

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Basic information

Entry
Database: PDB / ID: 9kue
TitleCrystal structure of the soluble green pigment protein from Tettigonia cantans
Components(Dibilinoxanthinin ...) x 3
KeywordsTRANSPORT PROTEIN / carotenoid binding / bilin binding / carotenoid carrier / vitellogenin / bichromoprotein
Function / homology: / AZIDE ION / Chem-LUT / DIUNDECYL PHOSPHATIDYL CHOLINE
Function and homology information
Biological speciesTettigonia cantans (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsSluchanko, N.N. / Egorkin, N.A. / 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 soluble green pigment protein from Tettigonia cantans
Authors: Sluchanko, N.N. / Egorkin, N.A. / Varfolomeeva, L.A. / Popov, V.O. / Boyko, K.M.
History
DepositionDec 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dibilinoxanthinin (DBXN)
B: Dibilinoxanthinin (DBXN)
C: Dibilinoxanthinin (DBXN)
D: Dibilinoxanthinin (DBXN)
E: Dibilinoxanthinin (DBXN)
F: Dibilinoxanthinin (DBXN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,87120
Polymers77,3446
Non-polymers5,52714
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, cross-linking, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25800 Å2
ΔGint-79 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.570, 87.256, 167.609
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Dibilinoxanthinin ... , 3 types, 6 molecules ADBECF

#1: Protein Dibilinoxanthinin (DBXN)


Mass: 12398.976 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tettigonia cantans (insect) / Tissue: integuments
#2: Protein Dibilinoxanthinin (DBXN)


Mass: 7682.458 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tettigonia cantans (insect) / Tissue: integuments
#3: Protein Dibilinoxanthinin (DBXN)


Mass: 18590.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tettigonia cantans (insect) / Tissue: integuments

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Non-polymers , 5 types, 188 molecules

#4: Chemical ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN


Mass: 568.871 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: N3
#6: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H65NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#7: Chemical ChemComp-A1L6M / 3-[5-[(~{Z})-(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[(~{Z})-[4-(hydroxymethyl)-3-(3-hydroxy-3-oxopropyl)-5-[(~{Z})-[3-methyl-5-oxidanylidene-4-[(1~{S},4~{E},8~{Z})-5,9,13-trimethyl-1-oxidanyl-tetradeca-4,8,12-trienyl]pyrrol-2-ylidene]methyl]pyrrol-2-ylidene]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid


Mass: 823.028 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C48H62N4O8 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl pH 8.5, 0.2 M MgCl2, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Nov 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.99→47.57 Å / Num. obs: 48786 / % possible obs: 99.9 % / Redundancy: 24.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.307 / Rpim(I) all: 0.062 / Rrim(I) all: 0.313 / Χ2: 1.04 / Net I/σ(I): 8.6 / Num. measured all: 1216322
Reflection shellResolution: 1.99→2.04 Å / % possible obs: 99.2 % / Redundancy: 14.2 % / Rmerge(I) obs: 1.796 / Num. measured all: 49285 / Num. unique obs: 3470 / CC1/2: 0.412 / Rpim(I) all: 0.489 / Rrim(I) all: 1.863 / Χ2: 1.08 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→31.6 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.91 / SU B: 13.61 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26679 2456 5 %RANDOM
Rwork0.22318 ---
obs0.22536 46216 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.229 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å20 Å2-0 Å2
2---1.28 Å20 Å2
3----0.86 Å2
Refinement stepCycle: 1 / Resolution: 1.99→31.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5259 0 390 174 5823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0125748
X-RAY DIFFRACTIONr_bond_other_d0.0050.0165392
X-RAY DIFFRACTIONr_angle_refined_deg2.1071.8267775
X-RAY DIFFRACTIONr_angle_other_deg1.0161.75812438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9665676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.732596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69210883
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1060.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026728
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021270
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_it1.3861.4952728
X-RAY DIFFRACTIONr_mcbond_other1.3851.4972729
X-RAY DIFFRACTIONr_mcangle_it2.2382.693396
X-RAY DIFFRACTIONr_mcangle_other2.2382.6913397
X-RAY DIFFRACTIONr_scbond_it1.851.683020
X-RAY DIFFRACTIONr_scbond_other1.7161.6693007
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7823.0064374
X-RAY DIFFRACTIONr_long_range_B_refined4.84814.545897
X-RAY DIFFRACTIONr_long_range_B_other4.82614.45865
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.991→2.042 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 189 -
Rwork0.348 3261 -
obs--99.08 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4172-0.24660.52171.1189-0.48422.67540.0080.22020.2803-0.3386-0.0812-0.0682-0.13420.22630.07320.13630.00210.02460.2010.01720.167814.3034-52.75488.0033
21.79711.4856-1.23164.2726-1.73962.9150.1666-0.2310.06690.4839-0.0783-0.1409-0.15280.4706-0.08830.05610.0069-0.01510.3051-0.00730.169222.4525-59.478833.2724
31.59980.6348-0.47322.171-0.74071.6718-0.1117-0.0243-0.1187-0.11790.0050.01770.4990.02610.10670.1560.01740.03010.0850.00720.09558.0181-75.916525.0925
40.61880.18190.26421.46320.57953.1666-0.00020.1118-0.039-0.1807-0.06820.1910.028-0.24790.06840.02740.0088-0.01190.19650.00620.1749-3.2331-51.671213.8695
52.4761.72141.54683.83891.69373.24570.0511-0.15460.18340.2796-0.0971-0.0667-0.4623-0.020.0460.1728-0.00090.01330.1325-0.00460.14514.8209-38.326436.0187
61.95640.4378-0.13682.7003-0.57982.6931-0.02670.18170.498-0.0928-0.1516-0.2091-1.10340.42890.17830.5271-0.1382-0.01990.1710.08370.28279.7042-25.789916.9235
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 201
2X-RAY DIFFRACTION2B1 - 67
3X-RAY DIFFRACTION3C4 - 203
4X-RAY DIFFRACTION4D1 - 202
5X-RAY DIFFRACTION5E1 - 67
6X-RAY DIFFRACTION6F4 - 202

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