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- PDB-8ow6: PERIDININ-CHLOROPHYLL-PROTEIN OF HETEROCAPSA PYGMAEA, 100K -

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Basic information

Entry
Database: PDB / ID: 8ow6
TitlePERIDININ-CHLOROPHYLL-PROTEIN OF HETEROCAPSA PYGMAEA, 100K
Components(Peridinin-chl a ...) x 2
KeywordsPHOTOSYNTHESIS / Light Harvesting / Carotenoid / Chlorophyll / Lipid / Dinoflagellates
Function / homology
Function and homology information


light-harvesting complex / chlorophyll binding
Similarity search - Function
Peridinin-chlorophyll A binding protein / Peridinin-chlorophyll A binding superfamily / Peridinin-chlorophyll A binding protein
Similarity search - Domain/homology
CHLOROPHYLL A / : / PERIDININ / PHOSPHATE ION / : / Peridinin-chl a protein
Similarity search - Component
Biological speciesHeterocapsa pygmaea (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsHofmann, E. / Schulte, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB480 Germany
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2024
Title: Structural and spectroscopic characterization of the peridinin-chlorophyll a-protein (PCP) complex from Heterocapsa pygmaea (HPPCP).
Authors: Schulte, T. / Magdaong, N.C.M. / Di Valentin, M. / Agostini, A. / Tait, C.E. / Niedzwiedzki, D.M. / Carbonera, D. / Hofmann, E.
History
DepositionApr 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Oct 16, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peridinin-chl a protein
B: Peridinin-chl a protein
C: Peridinin-chl a protein
D: Peridinin-chl a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,36632
Polymers62,7574
Non-polymers17,60828
Water14,754819
1
A: Peridinin-chl a protein
B: Peridinin-chl a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,28718
Polymers31,3792
Non-polymers8,90816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Peridinin-chl a protein
D: Peridinin-chl a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,07814
Polymers31,3792
Non-polymers8,70012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.610, 90.610, 155.610
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number149
Space group name H-MP312
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: -y,-x,-z
#5: -x+y,y,-z
#6: x,x-y,-z

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Components

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Peridinin-chl a ... , 2 types, 4 molecules ACBD

#1: Protein Peridinin-chl a protein


Mass: 15707.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Heterocapsa pygmaea (eukaryote) / Strain: UCSB-5M29 / References: UniProt: Q9FEY4
#2: Protein Peridinin-chl a protein


Mass: 15670.832 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Heterocapsa pygmaea (eukaryote) / Strain: UCSB-5M29

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Non-polymers , 7 types, 847 molecules

#3: Chemical
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PID / PERIDININ


Mass: 630.810 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C39H50O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-W4O / [(2~{S})-3-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-[[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-[(6~{Z},9~{Z},12~{Z},15~{Z})-octadeca-6,9,12,15-tetraenoyl]oxy-propyl] (6~{Z},9~{Z},12~{Z},15~{Z})-octadeca-6,9,12,15-tetraenoate


Mass: 933.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C51H80O15 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 819 / 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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.82 M NaH2PO4 1.24 M K2HPO4 100 mM Na-acetate at pH 5.5 100 mM LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9788 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.2→43.5 Å / Num. obs: 227100 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 15.7 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.119 / Net I/σ(I): 8.11
Reflection shellResolution: 1.2→1.23 Å / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 1.31 / Num. unique obs: 16634 / CC1/2: 0.386 / Rrim(I) all: 0.942

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSVERSION Feb 5, 2021 BUILT=20210323data reduction
XSCALEVERSION Feb 5, 2021 BUILT=20210323data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→43.5 Å / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 27.0822
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1705 2143 0.94 %
Rwork0.1489 224957 -
obs0.1626 227100 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.04 Å2
Refinement stepCycle: LAST / Resolution: 1.2→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 1268 819 6485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01415957
X-RAY DIFFRACTIONf_angle_d1.0278227
X-RAY DIFFRACTIONf_chiral_restr0.0634835
X-RAY DIFFRACTIONf_plane_restr0.01251034
X-RAY DIFFRACTIONf_dihedral_angle_d28.0551114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.230.24571380.247314855X-RAY DIFFRACTION98.59
1.23-1.260.26741430.23714907X-RAY DIFFRACTION98.82
1.26-1.290.25811390.221614936X-RAY DIFFRACTION98.95
1.29-1.330.22421430.215314929X-RAY DIFFRACTION98.93
1.33-1.370.21161430.208214970X-RAY DIFFRACTION99.01
1.37-1.420.19451430.195614864X-RAY DIFFRACTION99.01
1.42-1.480.21061410.189714988X-RAY DIFFRACTION99.05
1.48-1.550.20641440.181214940X-RAY DIFFRACTION99.01
1.55-1.630.22231380.177514989X-RAY DIFFRACTION99.05
1.63-1.730.20581450.172315030X-RAY DIFFRACTION99.02
1.73-1.860.18961380.171614982X-RAY DIFFRACTION99.09
1.86-2.050.18081480.168115058X-RAY DIFFRACTION98.99
2.05-2.350.16791450.151715054X-RAY DIFFRACTION98.96
2.35-2.960.16441430.13915101X-RAY DIFFRACTION98.92
2.96-43.50.15631480.127715358X-RAY DIFFRACTION98.68

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