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- PDB-4lcz: Crystal structure of a multilayer-packed major light-harvesting c... -

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Basic information

Entry
Database: PDB / ID: 4lcz
TitleCrystal structure of a multilayer-packed major light-harvesting complex
ComponentsMajor chlorophyll a/b binding protein LHCb1.3
KeywordsMEMBRANE PROTEIN / Light collecting / Photon protection / Grana stacking / Chlorophyll binding
Function / homology
Function and homology information


photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / metal ion binding
Similarity search - Function
Chlorophyll a-b binding protein / Chlorophyll a/b binding protein domain / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CACODYLATE ION / CHLOROPHYLL B / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-LUT / Chem-NEX / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWan, T. / Li, M. / Chang, W.R.
CitationJournal: Mol Plant / Year: 2014
Title: Crystal structure of a multilayer packed major light-harvesting complex: implications for grana stacking in higher plants.
Authors: Wan, T. / Li, M. / Zhao, X. / Zhang, J. / Liu, Z. / Chang, W.
History
DepositionJun 24, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Advisory / Data collection / Category: database_PDB_caveat / pdbx_validate_chiral
Revision 2.0Aug 24, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / citation ...chem_comp / citation / database_2 / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_site
Item: _chem_comp.formula / _chem_comp.pdbx_synonyms ..._chem_comp.formula / _chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_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_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major chlorophyll a/b binding protein LHCb1.3
B: Major chlorophyll a/b binding protein LHCb1.3
C: Major chlorophyll a/b binding protein LHCb1.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,40470
Polymers72,3883
Non-polymers46,01667
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)199.195, 115.097, 109.597
Angle α, β, γ (deg.)90.00, 113.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-322-

NA

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Major chlorophyll a/b binding protein LHCb1.3


Mass: 24129.248 Da / Num. of mol.: 3 / Fragment: UNP residues 44-267 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: B3WFZ6, UniProt: P12333*PLUS

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Non-polymers , 9 types, 223 molecules

#2: 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.: 6 / Source method: obtained synthetically / Formula: C40H56O2
#3: Chemical ChemComp-NEX / (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL / (3S,5R,6R,3'S,5'R,6'S)-5',6'-EPOXY-6,7-DIDEHYDRO- 5,6,5',6'-TETRAHYDRO-BETA,BETA-CAROTENE-3,5,3'-TRIOL / 9'-CIS-NEOXANTHIN


Mass: 600.870 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H56O4
#4: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#5: Chemical
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#6: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#7: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6AsO2
#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#9: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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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: 7.97 Å3/Da / Density % sol: 84.58 %
Crystal growTemperature: 291 K / pH: 6.5
Details: 2 mg/ml DGDG, 100mM di-sodium cacodylate, 10-12%(w/v) PEG2000, 20-50mM zinc acetate , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.96
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 69844 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.643 / % possible all: 98.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RWT

1rwt


Resolution: 2.6→43.45 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 26.38 / Stereochemistry target values: ML
Details: MATTHEW COEFFICIENT AND SOLVENT CONTENT HAVE BEEN CALCULATED BY SFCHECK CONTAINED IN THE CCP4 SUITE.
RfactorNum. reflection% reflection
Rfree0.258 3045 5.02 %
Rwork0.25 --
obs0.251 60663 86.4 %
all-60673 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.9124 Å20 Å20.3 Å2
2--6.6287 Å20 Å2
3----2.1755 Å2
Refinement stepCycle: LAST / Resolution: 2.6→43.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4737 0 3123 156 8016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018375
X-RAY DIFFRACTIONf_angle_d2.19411929
X-RAY DIFFRACTIONf_dihedral_angle_d22.3183482
X-RAY DIFFRACTIONf_chiral_restr0.118989
X-RAY DIFFRACTIONf_plane_restr0.0051353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.63770.2752190.2844484X-RAY DIFFRACTION16
2.6377-2.6810.2231430.2788834X-RAY DIFFRACTION27
2.681-2.72720.3125560.2821180X-RAY DIFFRACTION39
2.7272-2.77680.3521700.2731663X-RAY DIFFRACTION55
2.7768-2.83020.28841220.28352377X-RAY DIFFRACTION78
2.8302-2.88790.30461470.27412838X-RAY DIFFRACTION93
2.8879-2.95070.28131550.26872976X-RAY DIFFRACTION98
2.9507-3.01930.2871270.26663004X-RAY DIFFRACTION99
3.0193-3.09480.27821630.26922975X-RAY DIFFRACTION100
3.0948-3.17850.2761800.26133015X-RAY DIFFRACTION100
3.1785-3.2720.25451830.24242996X-RAY DIFFRACTION100
3.272-3.37760.24051740.2353029X-RAY DIFFRACTION100
3.3776-3.49820.22791520.2263021X-RAY DIFFRACTION100
3.4982-3.63820.23951410.23353036X-RAY DIFFRACTION100
3.6382-3.80370.24531760.22663007X-RAY DIFFRACTION100
3.8037-4.00410.21961630.22783021X-RAY DIFFRACTION100
4.0041-4.25480.24091750.23263017X-RAY DIFFRACTION100
4.2548-4.5830.25871650.23793013X-RAY DIFFRACTION100
4.583-5.04360.23821600.23063010X-RAY DIFFRACTION100
5.0436-5.77190.25221500.26163080X-RAY DIFFRACTION100
5.7719-7.26650.25911620.27233020X-RAY DIFFRACTION99
7.2665-43.46150.30391620.28863022X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 11.4897 Å / Origin y: 53.4186 Å / Origin z: 24.9062 Å
111213212223313233
T0.0368 Å2-0.0126 Å2-0.0032 Å2-0.0598 Å2-0.0263 Å2---0.0455 Å2
L2.1119 °2-0.198 °20.2494 °2-1.8646 °20.0201 °2--1.5702 °2
S0.1963 Å °-0.2008 Å °-0.0479 Å °0.1189 Å °0.1812 Å °-0.1152 Å °0.0152 Å °0.0496 Å °-0.2123 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA14 - 458
2X-RAY DIFFRACTION1allC14 - 451
3X-RAY DIFFRACTION1allB14 - 447

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