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- PDB-6a2w: Crystal structure of fucoxanthin chlorophyll a/c complex from Pha... -

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Basic information

Entry
Database: PDB / ID: 6a2w
TitleCrystal structure of fucoxanthin chlorophyll a/c complex from Phaeodactylum tricornutum
ComponentsProtein fucoxanthin chlorophyl a/c protein
KeywordsPHOTOSYNTHESIS / Light-harvesting / Fucoxanthin / Diatom
Function / homology
Function and homology information


light-harvesting complex / photosynthesis, light harvesting / plastid / chlorophyll binding / membrane / identical protein binding
Similarity search - Function
Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein
Similarity search - Domain/homology
Chem-A86 / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll c1 / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Unknown ligand / Protein fucoxanthin chlorophyl a/c protein
Similarity search - Component
Biological speciesPhaeodactylum tricornutum CCAP 1055/1 (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsWang, W. / Yu, L.J. / Kuang, T.Y. / Shen, J.R.
CitationJournal: Science / Year: 2019
Title: Structural basis for blue-green light harvesting and energy dissipation in diatoms.
Authors: Wang, W. / Yu, L.J. / Xu, C. / Tomizaki, T. / Zhao, S. / Umena, Y. / Chen, X. / Qin, X. / Xin, Y. / Suga, M. / Han, G. / Kuang, T. / Shen, J.R.
History
DepositionJun 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 2.0Feb 20, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.2Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_chiral
Item: _chem_comp.formula / _chem_comp.pdbx_synonyms ..._chem_comp.formula / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein fucoxanthin chlorophyl a/c protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,50934
Polymers18,3431
Non-polymers16,16633
Water1,44180
1
A: Protein fucoxanthin chlorophyl a/c protein
hetero molecules

A: Protein fucoxanthin chlorophyl a/c protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,01868
Polymers36,6862
Non-polymers32,33366
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)47.749, 115.718, 141.261
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein fucoxanthin chlorophyl a/c protein / Protein fucoxanthin chlorophyll a/c protein


Mass: 18342.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Phaeodactylum tricornutum CCAP 1055/1 (Diatom)
Strain: CCAP 1055/1 / References: UniProt: B7FRW2

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Sugars , 3 types, 6 molecules

#8: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#9: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15
#11: Sugar
ChemComp-SOG / octyl 1-thio-beta-D-glucopyranoside / 2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL / 1-S-OCTYL-BETA-D-THIOGLUCOSIDE / octyl 1-thio-beta-D-glucoside / octyl 1-thio-D-glucoside / octyl 1-thio-glucoside / N-Octyl beta-D-thioglucopyranoside


Type: D-saccharide / Mass: 308.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C14H28O5S / Comment: detergent*YM

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Non-polymers , 9 types, 107 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-A86 / (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate / Fucoxanthin / Fucoxanthin


Mass: 658.906 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C42H58O6
#4: Chemical ChemComp-DD6 / (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol / Diadinoxanthin / Diadinoxanthin


Mass: 582.855 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H54O3
#5: Chemical
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#6: Chemical ChemComp-KC2 / Chlorophyll c2 / Chlorophyll c


Mass: 608.926 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H28MgN4O5
#7: Chemical ChemComp-KC1 / Chlorophyll c1 / Chlorophyll c


Mass: 610.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H30MgN4O5
#10: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#12: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 7 / Source method: obtained synthetically
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsThere are some cylindrical shape electron densities around the pigment-protein complex, and it is ...There are some cylindrical shape electron densities around the pigment-protein complex, and it is hard to confirm whether they are detergents or lipid tails. Thus, these densities are assigned as UNL (unknown objects) tentatively.

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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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 293 K / Method: microbatch
Details: PEG 1000, calcium chloride, n-octal-D-thioglucoside, 4-Morpholineethanesulfonic acid hydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→19.983 Å / Num. obs: 36704 / % possible obs: 66.97 % / Redundancy: 2 % / Biso Wilson estimate: 28.79 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.02486 / Rpim(I) all: 0.02486 / Rrim(I) all: 0.03515 / Net I/σ(I): 11.55
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.7551 / Mean I/σ(I) obs: 0.95 / Num. unique obs: 1157 / CC1/2: 0.721 / Rpim(I) all: 0.7551 / Rrim(I) all: 1.068 / % possible all: 31.86

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→19.983 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.03
RfactorNum. reflection% reflection
Rfree0.1968 1860 7.55 %
Rwork0.1748 --
obs-24631 67.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.62 Å2 / Biso mean: 43.66 Å2 / Biso min: 13.51 Å2
Refinement stepCycle: final / Resolution: 1.8→19.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 0 1130 80 2496
Biso mean--49.35 50.24 -
Num. residues----166
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.84870.2578660.198681287831
1.8487-1.9030.2336760.206924100036
1.903-1.96440.2507850.19951041112641
1.9644-2.03450.2252950.19551167126246
2.0345-2.11590.27151070.18521303141051
2.1159-2.21210.20041190.17471456157556
2.2121-2.32860.22941360.18141660179664
2.3286-2.47420.20371510.17911858200972
2.4742-2.66480.19111710.18122093226480
2.6648-2.93230.18721970.17772409260693
2.9323-3.35480.21142140.169726262840100
3.3548-4.22020.1622180.145226642882100
4.2202-19.98460.20152250.184627582983100
Refinement TLS params.Method: refined / Origin x: -21.4942 Å / Origin y: -2.4241 Å / Origin z: 17.2439 Å
111213212223313233
T0.2265 Å20.0265 Å2-0.0026 Å2-0.1172 Å2-0.0717 Å2--0.1447 Å2
L2.2195 °20.3234 °20.3617 °2-1.2048 °2-0.2395 °2--4.0586 °2
S0.0816 Å °0.1258 Å °-0.0825 Å °0.0298 Å °-0.0035 Å °-0.0005 Å °0.3406 Å °0.1025 Å °-0.0056 Å °
Refinement TLS groupSelection details: all

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