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Basic information

Entry
Database: PDB / ID: 1kzu
TitleINTEGRAL MEMBRANE PERIPHERAL LIGHT HARVESTING COMPLEX FROM RHODOPSEUDOMONAS ACIDOPHILA STRAIN 10050
Components(LIGHT HARVESTING PROTEIN B-800/850) x 2
KeywordsLIGHT-HARVESTING PROTEIN / ANTENNA COMPLEX / LH2 COMPLEX / BACTERIOCHLOROPHYLL / PURPLE BACTERIA
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 / Rhodopin b-D-glucoside / Light-harvesting protein B-800/850 alpha chain / Light-harvesting protein B-800/850 beta chain
Similarity search - Component
Biological speciesRhodoblastus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.5 Å
AuthorsCogdell, R.J. / Freer, A.A. / Isaacs, N.W. / Hawthornthwaite-Lawless, A.M. / Mcdermott, G. / Papiz, M.Z. / Prince, S.M.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Apoprotein structure in the LH2 complex from Rhodopseudomonas acidophila strain 10050: modular assembly and protein pigment interactions.
Authors: Prince, S.M. / Papiz, M.Z. / Freer, A.A. / McDermott, G. / Hawthornthwaite-Lawless, A.M. / Cogdell, R.J. / Isaacs, N.W.
#1: Journal: Photochem.Photobiol. / Year: 1996
Title: Structure-Based Calculations on the Optical Spectra of the Lh2 Bacteriochlorophyll-Protein Complex from Rhodopseudomonas Acidophila
Authors: Sauer, K. / Cogdell, R.J. / Prince, S.M. / Freer, A. / Isaacs, N.W. / Scheer, H.
#2: Journal: Structure / Year: 1996
Title: Pigment-Pigment Interactions and Energy Transfer in the Antenna Complex of the Photosynthetic Bacterium Rhodopseudomonas Acidophila
Authors: Freer, A. / Prince, S. / Sauer, K. / Papiz, M. / Hawthornthwaite-Lawless, A. / Mcdermott, G. / Cogdell, R. / Isaacs, N.W.
#3: Journal: Trends Plant Sci. / Year: 1996
Title: A Model for the Photosynthetic Apparatus of Purple Bacteria
Authors: Papiz, M.Z. / Prince, S.M. / Hawthornthwaite-Lawless, A.M. / Mcdermott, G. / Freer, A. / Isaacs, N.W. / Cogdell, R.J.
#4: Journal: Nature / Year: 1995
Title: Crystal Structure of an Integral Membrane Light-Harvesting Complex from Photosynthetic Bacteria
Authors: Mcdermott, G. / Prince, S.M. / Freer, A.A. / Hawthornthwaite-Lawless, A.M. / Papiz, M.Z. / Cogdell, R.J. / Isaacs, N.W.
#5: Journal: Curr.Opin.Struct.Biol. / Year: 1995
Title: Light-Harvesting Mechanisms in Purple Photosynthetic Bacteria
Authors: Isaacs, N.W. / Cogdell, R.J. / Freer, A.A. / Prince, S.M.
History
DepositionAug 31, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 30, 2016Group: Non-polymer description
Revision 2.0Jun 5, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / software / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _software.name / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 6, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / pdbx_validate_symm_contact

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIGHT HARVESTING PROTEIN B-800/850
B: LIGHT HARVESTING PROTEIN B-800/850
D: LIGHT HARVESTING PROTEIN B-800/850
E: LIGHT HARVESTING PROTEIN B-800/850
G: LIGHT HARVESTING PROTEIN B-800/850
H: LIGHT HARVESTING PROTEIN B-800/850
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,23121
Polymers30,7386
Non-polymers12,49415
Water91951
1
A: LIGHT HARVESTING PROTEIN B-800/850
B: LIGHT HARVESTING PROTEIN B-800/850
D: LIGHT HARVESTING PROTEIN B-800/850
E: LIGHT HARVESTING PROTEIN B-800/850
G: LIGHT HARVESTING PROTEIN B-800/850
H: LIGHT HARVESTING PROTEIN B-800/850
hetero molecules

A: LIGHT HARVESTING PROTEIN B-800/850
B: LIGHT HARVESTING PROTEIN B-800/850
D: LIGHT HARVESTING PROTEIN B-800/850
E: LIGHT HARVESTING PROTEIN B-800/850
G: LIGHT HARVESTING PROTEIN B-800/850
H: LIGHT HARVESTING PROTEIN B-800/850
hetero molecules

A: LIGHT HARVESTING PROTEIN B-800/850
B: LIGHT HARVESTING PROTEIN B-800/850
D: LIGHT HARVESTING PROTEIN B-800/850
E: LIGHT HARVESTING PROTEIN B-800/850
G: LIGHT HARVESTING PROTEIN B-800/850
H: LIGHT HARVESTING PROTEIN B-800/850
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,69463
Polymers92,21318
Non-polymers37,48145
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Unit cell
Length a, b, c (Å)120.300, 120.300, 296.200
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
11E-45-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(0.766044, -0.642788), (0.642788, 0.766044), (1)
2given(0.173648, -0.984808), (0.984808, 0.173648), (1)
DetailsTHE CELL IS A HEXAGONALLY INDEXED RHOMBOHEDRAL CELL. THE DEPOSITORS PROVIDED ONE-THIRD OF THE ASYMMETRIC UNIT. THE REMAINING TWO-THIRDS WERE GENERATED BY THE PDB USING THE MTRIX TRANSFORMATIONS SO THAT THE ENTRY CONTAINS A COMPLETE ASYMMETRIC UNIT. ASSOCIATION OF CHAIN IDENTIFIERS AND HET ATOMS PROTEIN CHAIN HET AND SOLVENT CHAIN A, B C D, E F G, H I

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Components

#1: Protein LIGHT HARVESTING PROTEIN B-800/850 / LH2


Mass: 5686.733 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rhodoblastus acidophilus (bacteria) / Strain: 10050 / References: UniProt: P26789
#2: Protein/peptide LIGHT HARVESTING PROTEIN B-800/850 / LH2


Mass: 4559.203 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rhodoblastus acidophilus (bacteria) / Strain: 10050 / References: UniProt: P26790
#3: Sugar
ChemComp-RG1 / Rhodopin b-D-glucoside / (3E)-3,4-didehydro-1',2'-dihydro-psi,psi-caroten-1'-yl beta-D-glucopyranoside


Type: D-saccharide / Mass: 715.013 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C46H66O6
#4: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 9

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Sample preparation

CrystalDensity % sol: 73 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 9.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.9 Mphosphate1drop
23 %benzamidine hydrochloride1drop
32.4 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.5→12 Å / Num. obs: 28574 / % possible obs: 98.9 % / Redundancy: 2.3 % / Biso Wilson estimate: 57.77 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 5.9
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 1.9 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.5→12 Å / Rfactor Rfree error: 0.028 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1307 4.6 %RANDOM
Rwork0.227 ---
obs0.227 28287 98.71 %-
Displacement parametersBiso mean: 34.52 Å2
Baniso -1Baniso -2Baniso -3
1--4.3404 Å2-13.5633 Å20 Å2
2---4.3404 Å20 Å2
3---8.6809 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.45 Å
Luzzati d res low-9.1 Å
Luzzati sigma a-0.4 Å
Refinement stepCycle: LAST / Resolution: 2.5→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2094 0 816 51 2961
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.02
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_deg2.12
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.97
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.961.5
X-RAY DIFFRACTIONx_mcangle_it7.322
X-RAY DIFFRACTIONx_scbond_it4.982
X-RAY DIFFRACTIONx_scangle_it7.672.5
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.085
RfactorNum. reflection% reflection
Rfree0.387 138 3.89 %
Rwork0.302 3156 -
obs--92.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PRO 1KZUTOPHCSDX.PRO 1KZU
X-RAY DIFFRACTION2PARAM_ADDN.LH2 1KZUTOPH_BCHL.LH2 1KZU
X-RAY DIFFRACTION3TOPH_CAR.LH2
X-RAY DIFFRACTION4TOPH_CARC.LH2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 27855 / Rfactor Rfree: 0.253
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.97
LS refinement shell
*PLUS
Rfactor obs: 0.302

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