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- PDB-8ii8: X-ray crystal structure of pink-colored protein from Pleurotus sa... -

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Basic information

Entry
Database: PDB / ID: 8ii8
TitleX-ray crystal structure of pink-colored protein from Pleurotus salmoneostramineus in complex with natural chromophore
ComponentsChromoprotein
KeywordsLIPID BINDING PROTEIN / Chromoprotein / Mushroom
Function / homologyACETYL GROUP / : / Chromoprotein
Function and homology information
Biological speciesPleurotus salmoneostramineus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsIhara, M. / Fukuta, Y. / Shirasaka, N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K06175 Japan
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Crystal Structure of the Native Chromoprotein from Pleurotus salmoneostramineus Provides Insights into the Pigmentation Mechanism.
Authors: Ihara, M. / Tsuchida, N. / Sumida, M. / Himiyama, T. / Kitayama, T. / Shirasaka, N. / Fukuta, Y.
History
DepositionFeb 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1833
Polymers23,7361
Non-polymers4472
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, analytical centrifuge (sedimentation velocity experiment)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.879, 31.895, 107.416
Angle α, β, γ (deg.)90.000, 95.939, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-454-

HOH

21A-700-

HOH

31A-701-

HOH

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Components

#1: Protein Chromoprotein


Mass: 23736.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: N-terminal Met seems to be removed and substituted by acetyl group because we crystalized natural protein extracted from mushroom
Source: (natural) Pleurotus salmoneostramineus (fungus) / References: UniProt: A0A2Z5U5S2
#2: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#3: Chemical ChemComp-PW6 / (2E,5E,7Z,9E,11E,13E,15Z,17E,19Z,21E,23E)-24-methyl-25-oxohexacosa-2,5,7,9,11,13,15,17,19,21,23-undecaenoic acid / Dehydro laetiporic acid


Mass: 402.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H30O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.79 % / Description: Red colored rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: PEG4000, sodium formate, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.25→30.56 Å / Num. obs: 54840 / % possible obs: 99.1 % / Redundancy: 3.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.068 / Rrim(I) all: 0.098 / Χ2: 0.98 / Net I/av σ(I): 9.4 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
6.85-30.5630.06514.33550.9710.0640.0911.194.1
1.25-1.273.30.2763.826890.8960.2640.3830.8998.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSJan 10, 2022 BUILT=20220820data reduction
Aimless0.7.9data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: artificial helices without side chain

Resolution: 1.25→30.56 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.344 / SU ML: 0.027 / Cross valid method: FREE R-VALUE / ESU R: 0.042 / ESU R Free: 0.042
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1641 2826 5.153 %
Rwork0.1311 52013 -
all0.133 --
obs-54839 98.978 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.602 Å2
Baniso -1Baniso -2Baniso -3
1-0.684 Å2-0 Å20.017 Å2
2---1.524 Å2-0 Å2
3---0.818 Å2
Refinement stepCycle: LAST / Resolution: 1.25→30.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1657 0 33 312 2002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121803
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161659
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.6562458
X-RAY DIFFRACTIONr_angle_other_deg0.6171.5753923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1835255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.799525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75110319
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.6851071
X-RAY DIFFRACTIONr_chiral_restr0.0940.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02314
X-RAY DIFFRACTIONr_nbd_refined0.2590.2409
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.21423
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2907
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.2955
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2202
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1710.222
X-RAY DIFFRACTIONr_nbd_other0.2220.2101
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1920.244
X-RAY DIFFRACTIONr_mcbond_it1.2150.713933
X-RAY DIFFRACTIONr_mcbond_other1.2080.712932
X-RAY DIFFRACTIONr_mcangle_it1.5831.0761172
X-RAY DIFFRACTIONr_mcangle_other1.5871.0781173
X-RAY DIFFRACTIONr_scbond_it2.5181.056870
X-RAY DIFFRACTIONr_scbond_other2.5191.057869
X-RAY DIFFRACTIONr_scangle_it3.1061.4431270
X-RAY DIFFRACTIONr_scangle_other3.1051.4421271
X-RAY DIFFRACTIONr_lrange_it3.56619.4012255
X-RAY DIFFRACTIONr_lrange_other3.23613.8732156
X-RAY DIFFRACTIONr_rigid_bond_restr5.92833462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.2820.2082170.173795X-RAY DIFFRACTION98.5265
1.282-1.3170.2031860.1453766X-RAY DIFFRACTION99.6219
1.317-1.3560.1752000.133551X-RAY DIFFRACTION98.7365
1.356-1.3970.1582100.1233505X-RAY DIFFRACTION98.4889
1.397-1.4430.1581850.1263401X-RAY DIFFRACTION99.0334
1.443-1.4930.141760.1123311X-RAY DIFFRACTION99.4297
1.493-1.550.171580.1063216X-RAY DIFFRACTION99.4987
1.55-1.6130.1411620.1043062X-RAY DIFFRACTION99.4141
1.613-1.6840.1421620.1072981X-RAY DIFFRACTION98.8676
1.684-1.7660.1611600.1082814X-RAY DIFFRACTION99.5315
1.766-1.8610.1481450.1092676X-RAY DIFFRACTION99.331
1.861-1.9740.171290.1152562X-RAY DIFFRACTION99.116
1.974-2.110.1341440.1132397X-RAY DIFFRACTION99.1803
2.11-2.2780.1431180.1182242X-RAY DIFFRACTION99.2013
2.278-2.4940.1551030.1252049X-RAY DIFFRACTION98.7609
2.494-2.7860.1771020.1411859X-RAY DIFFRACTION98.7412
2.786-3.2120.171040.1471669X-RAY DIFFRACTION99.0503
3.212-3.9230.158890.1421396X-RAY DIFFRACTION98.8024
3.923-5.5030.211490.1481118X-RAY DIFFRACTION98.481
5.503-30.560.214270.211642X-RAY DIFFRACTION95.0284
Refinement TLS params.Method: refined / Origin x: 15.9462 Å / Origin y: 20.4845 Å / Origin z: 5.8452 Å
111213212223313233
T0.0023 Å2-0.0035 Å20.0017 Å2-0.0517 Å2-0.0012 Å2--0.0034 Å2
L0.6312 °2-0.4991 °20.1923 °2-1.5447 °2-0.9768 °2--1.577 °2
S0.0179 Å °-0.0091 Å °0.0454 Å °-0.0353 Å °-0.0436 Å °-0.0428 Å °0.0518 Å °0.0319 Å °0.0257 Å °
Refinement TLS groupSelection: ALL

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