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- PDB-1vcr: An icosahedral assembly of light-harvesting chlorophyll a/b prote... -

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Basic information

Entry
Database: PDB / ID: 1vcr
TitleAn icosahedral assembly of light-harvesting chlorophyll a/b protein complex from pea thylakoid membranes
ComponentsChlorophyll a-b binding protein AB80
KeywordsPHOTOSYNTHESIS / LHC-II / Icosahedron / chlorophyll / antenna / photosystem
Function / homology
Function and homology information


plastoglobule / photosynthesis, light harvesting in photosystem I / chloroplast envelope / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / metal ion 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
CHLOROPHYLL B / CHLOROPHYLL A / Chlorophyll a-b binding protein AB80, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 9.5 Å
AuthorsHino, T. / Kanamori, E. / Shen, J.-R. / Kouyama, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: An icosahedral assembly of the light-harvesting chlorophyll a/b protein complex from pea chloroplast thylakoid membranes.
Authors: Hino, T. / Kanamori, E. / Shen, J.R. / Kouyama, T.
History
DepositionMar 10, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_validate_chiral
Revision 2.0Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_chiral / struct_site
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chlorophyll a-b binding protein AB80
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,72813
Polymers24,9361
Non-polymers10,79212
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)360.646, 360.646, 360.646
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.809017, 0.30901699, 0.5), (0.30901699, 0.5, -0.80901699), (-0.5, 0.809017, 0.30901699)
3generate(0.5, 0.80901699, 0.309017), (0.809017, -0.30901699, -0.5), (-0.309017, 0.5, -0.809017)
4generate(0.5, 0.809017, -0.30901699), (0.809017, -0.309017, 0.5), (0.309017, -0.5, -0.80901699)
5generate(0.80901699, 0.309017, -0.5), (0.309017, 0.5, 0.80901699), (0.5, -0.80901699, 0.309017)

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Components

#1: Protein Chlorophyll a-b binding protein AB80 / LIGHT-HARVESTING CHLOROPHYLL A/B PROTEIN / LHCII type I CAB-AB80 / LHCP


Mass: 24936.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Tissue: thylakoid membrane / References: UniProt: P07371
#2: Chemical
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#3: Chemical
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C55H70MgN4O6

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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

Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Potassium chloride, PEG4000, Xylitol, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONSPring-8 BL38B121
SYNCHROTRONSPring-8 BL40B231
DetectorType: MARRESEARCH / Detector: CCD / Date: May 22, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 9.5→500 Å / Num. all: 2534 / Num. obs: 2532 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 296 Å2 / Rsym value: 0.085 / Net I/σ(I): 3
Reflection shellResolution: 9.5→10.1 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.499 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Personal communication with Prof. W. Kuhlbrandt. Nature 367, 614-621, (1994)

Resolution: 9.5→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.353 188 -RANDOM
Rwork0.379 ---
all-2241 --
obs-1935 86.3 %-
Displacement parametersBiso mean: 296 Å2
Refinement stepCycle: LAST / Resolution: 9.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms496 0 300 0 796

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