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- PDB-1lgh: CRYSTAL STRUCTURE OF THE LIGHT-HARVESTING COMPLEX II (B800-850) F... -

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Basic information

Entry
Database: PDB / ID: 1lgh
TitleCRYSTAL STRUCTURE OF THE LIGHT-HARVESTING COMPLEX II (B800-850) FROM RHODOSPIRILLUM MOLISCHIANUM
Components(LIGHT HARVESTING COMPLEX ...) x 2
KeywordsLIGHT HARVESTING COMPLEX / BACTERIOCHLOROPHYLL / DEXTER ENERGY TRANSFER / FOERSTER EXCITON TRANSFER MECHANISM / MEMBRANE PROTEIN / PHOTOSYNTHESIS
Function / homology
Function and homology information


organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / : / photosynthesis, light reaction / metal ion binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #250 / Light-harvesting complex / Light-harvesting Protein / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #250 / Light-harvesting complex / Light-harvesting Protein / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Few Secondary Structures / Irregular / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / UNDECYLAMINE-N,N-DIMETHYL-N-OXIDE / HEPTANE-1,2,3-TRIOL / LYCOPENE / Light-harvesting protein B-800/850 beta 1 chain / Light-harvesting protein B-800/850 alpha chain
Similarity search - Component
Biological speciesPhaeospirillum molischianum (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKoepke, J. / Hu, X. / Schulten, K. / Michel, H.
Citation
Journal: Structure / Year: 1996
Title: The crystal structure of the light-harvesting complex II (B800-850) from Rhodospirillum molischianum.
Authors: Koepke, J. / Hu, X. / Muenke, C. / Schulten, K. / Michel, H.
#1: Journal: Protein Sci. / Year: 1995
Title: Predicting the Structure of the Light-Harvesting Complex II of Rhodospirillum Molischianum
Authors: Hu, X. / Xu, D. / Hamer, K. / Schulten, K. / Koepke, J. / Michel, H.
History
DepositionMar 20, 1996Processing site: BNL
Revision 1.0Jun 5, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIGHT HARVESTING COMPLEX II
B: LIGHT HARVESTING COMPLEX II
D: LIGHT HARVESTING COMPLEX II
E: LIGHT HARVESTING COMPLEX II
G: LIGHT HARVESTING COMPLEX II
H: LIGHT HARVESTING COMPLEX II
J: LIGHT HARVESTING COMPLEX II
K: LIGHT HARVESTING COMPLEX II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,49060
Polymers44,2638
Non-polymers19,22752
Water1,15364
1
A: LIGHT HARVESTING COMPLEX II
B: LIGHT HARVESTING COMPLEX II
D: LIGHT HARVESTING COMPLEX II
E: LIGHT HARVESTING COMPLEX II
hetero molecules

A: LIGHT HARVESTING COMPLEX II
B: LIGHT HARVESTING COMPLEX II
D: LIGHT HARVESTING COMPLEX II
E: LIGHT HARVESTING COMPLEX II
hetero molecules

A: LIGHT HARVESTING COMPLEX II
B: LIGHT HARVESTING COMPLEX II
D: LIGHT HARVESTING COMPLEX II
E: LIGHT HARVESTING COMPLEX II
hetero molecules

A: LIGHT HARVESTING COMPLEX II
B: LIGHT HARVESTING COMPLEX II
D: LIGHT HARVESTING COMPLEX II
E: LIGHT HARVESTING COMPLEX II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,573124
Polymers88,52716
Non-polymers39,046108
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
MethodPQS
2
G: LIGHT HARVESTING COMPLEX II
H: LIGHT HARVESTING COMPLEX II
J: LIGHT HARVESTING COMPLEX II
K: LIGHT HARVESTING COMPLEX II
hetero molecules

G: LIGHT HARVESTING COMPLEX II
H: LIGHT HARVESTING COMPLEX II
J: LIGHT HARVESTING COMPLEX II
K: LIGHT HARVESTING COMPLEX II
hetero molecules

G: LIGHT HARVESTING COMPLEX II
H: LIGHT HARVESTING COMPLEX II
J: LIGHT HARVESTING COMPLEX II
K: LIGHT HARVESTING COMPLEX II
hetero molecules

G: LIGHT HARVESTING COMPLEX II
H: LIGHT HARVESTING COMPLEX II
J: LIGHT HARVESTING COMPLEX II
K: LIGHT HARVESTING COMPLEX II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,388116
Polymers88,52716
Non-polymers37,861100
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.600, 91.600, 209.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.707105, -0.707109), (0.707109, 0.707105), (1)13.41508, -32.48959, 0.02748
2given(0.954698, -0.297576), (-0.297576, -0.954698), (-1)2.19276, 13.62018, 105.85023
3given(0.461659, -0.887057), (-0.887057, -0.461659), (-1)24.69424, 40.61299, 105.82622
DetailsTHE DEPOSITOR PROVIDED ONE ALPHA CHAIN, ONE BETA CHAIN, AND ASSOCIATED HET GROUPS AND WATERS. USING THE TRANSFORMATIONS ON MTRIX RECORDS BELOW, THE PDB GENERATED THE COMPLETE ASYMMETRIC UNIT, CONSISTING OF FOUR ALPHA CHAINS, FOUR BETA CHAINS, AND ASSOCIATED HET GROUPS AND WATERS. ALPHA AND BETA CHAINS HET GROUPS AND WATERS A, B C D, E F G, H I J, K L

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Components

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LIGHT HARVESTING COMPLEX ... , 2 types, 8 molecules ADGJBEHK

#1: Protein
LIGHT HARVESTING COMPLEX II / LH II / B800/850


Mass: 5944.980 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Phaeospirillum molischianum (magnetotactic)
Strain: DSM 119 / References: UniProt: P97253
#2: Protein/peptide
LIGHT HARVESTING COMPLEX II / LH II / B800/850


Mass: 5120.873 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Phaeospirillum molischianum (magnetotactic)
Strain: DSM 119 / References: UniProt: P95673

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Non-polymers , 5 types, 116 molecules

#3: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#4: Chemical
ChemComp-LYC / LYCOPENE


Mass: 536.873 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H56
#5: Chemical
ChemComp-DET / UNDECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 215.375 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C13H29NO
#6: Chemical...
ChemComp-HTO / HEPTANE-1,2,3-TRIOL


Mass: 148.200 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C7H16O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.97 Å3/Da / Density % sol: 70.7 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlLH-21drop
23.2 %(w/v)HPTO1drop
34 Mammonium sulfate1drop
43.0-3.3 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.009
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 8, 1989 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 31941 / % possible obs: 89.1 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.097
Reflection shellResolution: 2.4→2.59 Å / Rmerge(I) obs: 0.311 / % possible all: 66.2

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AS A SEARCH MODEL FOR MOLECULAR REPLACEMENT SERVED A COMPUTATIONALLY MODELLED OCTAMER OF ALPHA,BETA-HETERODIMERS BASED ON A HOMOLOGY OF THE LATTER TO THE ALPHA,BETA-HETERODIMER FROM RPS. ACIDOPHILA.

Resolution: 2.4→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.232 -7 %
Rwork0.211 --
obs0.211 30309 87.2 %
Displacement parametersBiso mean: 47 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 1328 64 4488
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.943
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.81
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d7.097
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.814
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg7.097

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