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- PDB-2bhw: PEA LIGHT-HARVESTING COMPLEX II AT 2.5 ANGSTROM RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 2bhw
TitlePEA LIGHT-HARVESTING COMPLEX II AT 2.5 ANGSTROM RESOLUTION
ComponentsCHLOROPHYLL A-B BINDING PROTEIN AB80
KeywordsPHOTOSYNTHESIS / LHC-II / LIGHT-HARVESTING / MEMBRANE PROTEIN / CHLOROPHYLL / CHLOROPLAST / CHROMOPHORE / MEMBRANE / PHOSPHORYLATION / PHOTOSYSTEM I / PHOTOSYSTEM II / PLASTID / THYLAKOID / TRANSIT PEPTIDE / TRANSMEMBRANE
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 / 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
CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-LUX / Chem-NEX / Chem-XAT / Chlorophyll a-b binding protein AB80, chloroplastic
Similarity search - Component
Biological speciesPISUM SATIVUM (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsStandfuss, J. / Terwisscha van Scheltinga, A.C. / Lamborghini, M. / Kuehlbrandt, W.
Citation
Journal: Embo J. / Year: 2005
Title: Mechanisms of Photoprotection and Nonphotochemical Quenching in Pea Light-Harvesting Complex at 2.5 A Resolution.
Authors: Standfuss, J. / Terwisscha Van Scheltinga, A.C. / Lamborghini, M. / Kuehlbrandt, W.
#1: Journal: Nature / Year: 1994
Title: Atomic Model of Plant Light-Harvesting Complex by Electron Crystallography
Authors: Kuehlbrandt, W. / Wang, D.N. / Fujiyoshi, Y.
History
DepositionJan 19, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 24, 2019Group: Advisory / Data collection / Other
Category: database_PDB_caveat / pdbx_database_proc ...database_PDB_caveat / pdbx_database_proc / pdbx_database_status / pdbx_validate_chiral
Item: _pdbx_database_status.recvd_author_approval
Revision 2.0May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHLOROPHYLL A-B BINDING PROTEIN AB80
B: CHLOROPHYLL A-B BINDING PROTEIN AB80
C: CHLOROPHYLL A-B BINDING PROTEIN AB80
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,67063
Polymers74,7603
Non-polymers49,91060
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)211.400, 128.000, 62.000
Angle α, β, γ (deg.)90.00, 101.80, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.04114, -0.7272, -0.68519), (0.7173, -0.49889, 0.48641), (-0.69555, -0.47148, 0.54214)143.37335, 41.34145, 94.8063
2given(-0.04235, 0.71869, -0.69404), (-0.72416, -0.50066, -0.47426), (-0.68833, 0.48251, 0.54165)42.14149, 169.58359, 27.22568

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein CHLOROPHYLL A-B BINDING PROTEIN AB80 / LIGHT-HARVESTING COMPLEX II / LHCP / LHCII TYPE I CAB-AB80


Mass: 24920.049 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / Organ: CHLOROPLAST / Tissue: LEAVES / References: UniProt: P07371
#8: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 7 types, 78 molecules

#2: Chemical
ChemComp-LUX / (3R,3'R,6'S,9R,9'R,13R,13'S)-4',5'-DIDEHYDRO-5',6',7',8',9,9',10,10',11,11',12,12',13,13',14,14',15,15'-OCTADECAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL


Mass: 584.998 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H72O2
#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-XAT / (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / VIOLAXANTHIN


Mass: 600.870 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H56O4
#5: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#6: Chemical
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#7: 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
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE LIGHT-HARVESTING COMPLEX (LHC) FUNCTIONS AS A LIGHT RECEPTOR, IT CAPTURES AND DELIVERS ...THE LIGHT-HARVESTING COMPLEX (LHC) FUNCTIONS AS A LIGHT RECEPTOR, IT CAPTURES AND DELIVERS EXCITATION ENERGY TO PHOTOSYSTEMS WITH WHICH IT IS CLOSELY ASSOCIATED

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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: 4.1 Å3/Da / Density % sol: 69 %
Description: THE MODEL USED FOR MR WAS 3.4 ANGSTROM EM MAP. KUEHLBRANDT ET AL., 1994.
Crystal growpH: 5.5
Details: 14 % PEG 350 MMME 50 MM MES PH 5.5 10 % GLYCEROL, 20 MM NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 2, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 47867 / % possible obs: 85.6 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 103.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.99
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.7 / % possible all: 70.7

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Processing

Software
NameVersionClassification
TNT5Frefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EM MAP

Resolution: 2.5→50 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflectionSelection details
Rfree0.2412 990 2 %0.2201
Rwork0.2196 ---
all0.2201 ---
obs0.2196 47867 --
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5049 0 3303 21 8373
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01188292
X-RAY DIFFRACTIONt_angle_deg1.727124052
X-RAY DIFFRACTIONt_dihedral_angle_d17.2629760
X-RAY DIFFRACTIONt_incorr_chiral_ct12
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.01811462
X-RAY DIFFRACTIONt_gen_planes0.01150527
X-RAY DIFFRACTIONt_it1.666827720
X-RAY DIFFRACTIONt_nbd0.0922795
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact

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