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- PDB-1ijd: Crystallographic Structure of the LH3 Complex from Rhodopseudomon... -

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Basic information

Entry
Database: PDB / ID: 1ijd
TitleCrystallographic Structure of the LH3 Complex from Rhodopseudomonas acidophila strain 7050
Components(LIGHT-HARVESTING PROTEIN B-800/820, ...) x 2
KeywordsPHOTOSYNTHESIS / Pigment-protein complex / alpha-helix apoproteins / intergral membrane protein / light harvesting
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 / RHODOPINAL GLUCOSIDE / Light-harvesting protein B-800/820 alpha chain / Light-harvesting protein B-800/820 beta chain
Similarity search - Component
Biological speciesRhodoblastus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMcLuskey, K. / Prince, S.M. / Cogdell, R.J. / Isaacs, N.W.
Citation
Journal: Biochemistry / Year: 2001
Title: The crystallographic structure of the B800-820 LH3 light-harvesting complex from the purple bacteria Rhodopseudomonas acidophila strain 7050.
Authors: McLuskey, K. / Prince, S.M. / Cogdell, R.J. / Isaacs, N.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-ray Crystallographic Analysis of the B800-820 Light-harvesting Complex from Rhodopseudomonas acidophila Strain 7050
Authors: McLuskey, K. / Prince, S.M. / Cogdell, R.J. / Isaacs, N.W.
History
DepositionApr 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_bond.pdbx_aromatic_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIGHT-HARVESTING PROTEIN B-800/820, ALPHA CHAIN
B: LIGHT-HARVESTING PROTEIN B-800/820, BETA CHAIN
C: LIGHT-HARVESTING PROTEIN B-800/820, ALPHA CHAIN
D: LIGHT-HARVESTING PROTEIN B-800/820, BETA CHAIN
E: LIGHT-HARVESTING PROTEIN B-800/820, ALPHA CHAIN
F: LIGHT-HARVESTING PROTEIN B-800/820, BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,20421
Polymers30,9306
Non-polymers11,27415
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: LIGHT-HARVESTING PROTEIN B-800/820, ALPHA CHAIN
B: LIGHT-HARVESTING PROTEIN B-800/820, BETA CHAIN
C: LIGHT-HARVESTING PROTEIN B-800/820, ALPHA CHAIN
D: LIGHT-HARVESTING PROTEIN B-800/820, BETA CHAIN
E: LIGHT-HARVESTING PROTEIN B-800/820, ALPHA CHAIN
F: LIGHT-HARVESTING PROTEIN B-800/820, BETA CHAIN
hetero molecules

A: LIGHT-HARVESTING PROTEIN B-800/820, ALPHA CHAIN
B: LIGHT-HARVESTING PROTEIN B-800/820, BETA CHAIN
C: LIGHT-HARVESTING PROTEIN B-800/820, ALPHA CHAIN
D: LIGHT-HARVESTING PROTEIN B-800/820, BETA CHAIN
E: LIGHT-HARVESTING PROTEIN B-800/820, ALPHA CHAIN
F: LIGHT-HARVESTING PROTEIN B-800/820, BETA CHAIN
hetero molecules

A: LIGHT-HARVESTING PROTEIN B-800/820, ALPHA CHAIN
B: LIGHT-HARVESTING PROTEIN B-800/820, BETA CHAIN
C: LIGHT-HARVESTING PROTEIN B-800/820, ALPHA CHAIN
D: LIGHT-HARVESTING PROTEIN B-800/820, BETA CHAIN
E: LIGHT-HARVESTING PROTEIN B-800/820, ALPHA CHAIN
F: LIGHT-HARVESTING PROTEIN B-800/820, BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,61263
Polymers92,79118
Non-polymers33,82145
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area98360 Å2
ΔGint-618 kcal/mol
Surface area26720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)117.260, 117.260, 295.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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LIGHT-HARVESTING PROTEIN B-800/820, ... , 2 types, 6 molecules ACEBDF

#1: Protein LIGHT-HARVESTING PROTEIN B-800/820, ALPHA CHAIN / ANTENNA PIGMENT PROTEIN / ALPHA CHAIN


Mass: 5578.656 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: Photosynthetic purple bacteria / Source: (natural) Rhodoblastus acidophilus (bacteria) / Strain: 7050 / References: UniProt: P35089
#2: Protein/peptide LIGHT-HARVESTING PROTEIN B-800/820, BETA CHAIN / ANTENNA PIGMENT PROTEIN / BETA CHAIN


Mass: 4731.449 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: Photosynthetic purple bacteria / Source: (natural) Rhodoblastus acidophilus (bacteria) / Strain: 7050 / References: UniProt: P35094

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Sugars , 2 types, 6 molecules

#4: Sugar ChemComp-RPA / RHODOPINAL GLUCOSIDE


Type: saccharide / Mass: 731.012 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C46H66O7
#5: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 2 types, 51 molecules

#3: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


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


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 4.89 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.2
Details: potassium phosphate, benzamidine HCl, B-Octyl glucoside, sodium chloride, pH 9.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Details: McLuskey, K., (1999) Acta Crystallogr., Sect.D, 55, 885.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14.0 Mpotassium phosphate1droppH9.2
22.5 %(w/v)benzamidine hydrochloride1drop
32.3 Mammonium sulfate1reservoirpH9.7

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSRS PX9.610.87
SYNCHROTRONSRS PX9.620.87
Detector
TypeIDDetectorDateDetails
MARRESEARCH1IMAGE PLATEAug 29, 1999vertically focussing Rh coated Si mirror
MARRESEARCH2IMAGE PLATENov 23, 1999vertically focussing Rh coated Si mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1triangular single crystal Si monochromatorSINGLE WAVELENGTHMx-ray1
2triangular single crystal Si monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.8→42 Å / Num. obs: 18970 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 3.7 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 4.6
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.3 / % possible all: 94.7
Reflection
*PLUS
Highest resolution: 3 Å / % possible obs: 97 % / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 96.4 % / Rmerge(I) obs: 0.37

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Processing

Software
NameVersionClassification
AMoREphasing
RESTRAINrefinement
MOSFLMdata reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KZU (LH2 complex from Rps. acidophila strain 10050)

1kzu


Resolution: 3→42 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: Engh & Huber for protein, for cofactors; geometry derived from small molecule structures
RfactorNum. reflectionSelection details
Rfree0.256 770 equivalent hkl's as for 1KZU
Rwork0.243 --
all-16042 -
obs-15220 -
Displacement parametersBiso mean: 46.4 Å2
Refine analyzeLuzzati sigma a obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 3→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 780 42 2823
LS refinement shellResolution: 3→3.19 Å
RfactorNum. reflection
Rfree0.376 110
Rwork0.336 -
obs-2324
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / σ(F): 2 / Rfactor obs: 0.243
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 46.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_d0.021

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