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- PDB-1rwt: Crystal Structure of Spinach Major Light-harvesting complex at 2.... -

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Basic information

Entry
Database: PDB / ID: 1rwt
TitleCrystal Structure of Spinach Major Light-harvesting complex at 2.72 Angstrom Resolution
ComponentsChlorophyll A-B binding protein, chloroplast
KeywordsPHOTOSYNTHESIS / LIGHT-HARVESTING COMPLEX / MEMBRANE PROTEIN / PLANT
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / 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-LUT / Chem-NEX / Chem-XAT / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR in combination with real-space averaging refinement, extension / Resolution: 2.72 Å
AuthorsLiu, Z. / Yan, H. / Wang, K. / Kuang, T. / Zhang, J. / Gui, L. / An, X. / Chang, W.
CitationJournal: Nature / Year: 2004
Title: Crystal structure of spinach major light-harvesting complex at 2.72 A resolution
Authors: Liu, Z. / Yan, H. / Wang, K. / Kuang, T. / Zhang, J. / Gui, L. / An, X. / Chang, W.
History
DepositionDec 17, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4May 1, 2019Group: Advisory / Data collection / Category: database_PDB_caveat / pdbx_validate_chiral
Revision 1.5May 15, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _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_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_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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Mar 13, 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: Chlorophyll A-B binding protein, chloroplast
B: Chlorophyll A-B binding protein, chloroplast
C: Chlorophyll A-B binding protein, chloroplast
D: Chlorophyll A-B binding protein, chloroplast
E: Chlorophyll A-B binding protein, chloroplast
F: Chlorophyll A-B binding protein, chloroplast
G: Chlorophyll A-B binding protein, chloroplast
H: Chlorophyll A-B binding protein, chloroplast
I: Chlorophyll A-B binding protein, chloroplast
J: Chlorophyll A-B binding protein, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)419,135221
Polymers250,00310
Non-polymers169,132211
Water12,592699
1
A: Chlorophyll A-B binding protein, chloroplast
B: Chlorophyll A-B binding protein, chloroplast
C: Chlorophyll A-B binding protein, chloroplast
D: Chlorophyll A-B binding protein, chloroplast
E: Chlorophyll A-B binding protein, chloroplast
F: Chlorophyll A-B binding protein, chloroplast
G: Chlorophyll A-B binding protein, chloroplast
H: Chlorophyll A-B binding protein, chloroplast
I: Chlorophyll A-B binding protein, chloroplast
J: Chlorophyll A-B binding protein, chloroplast
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)2,514,8111326
Polymers1,500,02060
Non-polymers1,014,7911266
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area292210 Å2
ΔGint-2547 kcal/mol
Surface area901090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)261.787, 261.787, 660.498
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-634-

NA

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
Chlorophyll A-B binding protein, chloroplast / LHCII type I CAB / LHCP


Mass: 25000.330 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Tissue: leaf / References: UniProt: P12333

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Sugars , 2 types, 20 molecules

#2: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#8: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 8 types, 890 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: 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 / Lutein


Mass: 568.871 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H56O2
#5: 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 / Violaxanthin


Mass: 600.870 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C40H56O4
#6: 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.: 10 / Source method: obtained synthetically / Formula: C40H56O4
#7: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#9: Chemical...
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#10: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 80 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 699 / 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: 5.36 Å3/Da / Density % sol: 76.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: Citrate trisodium, beta-nonyl-glucoside, deoxy-bigchap, DGDG, Hepes, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6B11
SYNCHROTRONBSRF 3W1A21
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATENov 20, 2002
MARRESEARCH2IMAGE PLATEJun 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. all: 211079 / Num. obs: 191660 / % possible obs: 90.8 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.4
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.5 / Num. unique all: 9188 / % possible all: 79.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: SIR in combination with real-space averaging refinement, extension
Resolution: 2.72→10 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 557510.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 9326 4.9 %RANDOM
Rwork0.194 ---
all0.207 197822 --
obs0.194 188496 83 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.7972 Å2 / ksol: 0.37093 e/Å3
Displacement parametersBiso mean: 31.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å25.23 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.72→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16619 0 11721 699 29039
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d2.66
LS refinement shellResolution: 2.72→2.89 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 1204 4.7 %
Rwork0.233 24422 -
obs-26514 68.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP

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