1LGH

CRYSTAL STRUCTURE OF THE LIGHT-HARVESTING COMPLEX II (B800-850) FROM RHODOSPIRILLUM MOLISCHIANUM

PDB DOI: https://doi.org/10.2210/pdb1LGH/pdb

Classification: LIGHT HARVESTING COMPLEX
Organism(s): Magnetospirillum molischianum
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 1996-03-20 Released: 1997-06-05
Deposition Author(s): Koepke, J., Hu, X., Schulten, K., Michel, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.232
R-Value Work: 0.211
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The crystal structure of the light-harvesting complex II (B800-850) from Rhodospirillum molischianum.

Koepke, J., Hu, X., Muenke, C., Schulten, K., Michel, H.

(1996) Structure 4: 581-597

PubMed: 8736556 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(96)00063-9
Primary Citation of Related Structures:
1LGH

PubMed Abstract:
The light-harvesting complexes II (LH-2s) are integral membrane proteins that form ring-like structures, oligomers of alpha beta-heterodimers, in the photosynthetic membranes of purple bacteria. They contain a large number of chromophores organized optimally for light absorption and rapid light energy migration. Recently, the structure of the nonameric LH-2 of Rhodopseudomonas acidophila has been determined; we report here the crystal structure of the octameric LH-2 from Rhodospirillum molischianum. The unveiling of similarities and differences in the architecture of these proteins may provide valuable insight into the efficient energy transfer mechanisms of bacterial photosynthesis.

Organizational Affiliation

Max-Planck-Institut für Biochemie, Abteilung Molekulare Membranbiologie, Frankfurt, Germany.

Macromolecule Content

Total Structure Weight: 63.49 kDa
Atom Count: 4,488
Modelled Residue Count: 396
Deposited Residue Count: 404
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIGHT HARVESTING COMPLEX II	A, C [auth D], E [auth G], G [auth J]	56	Magnetospirillum molischianum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P97253 (Magnetospirillum molischianum) Explore P97253 Go to UniProtKB: P97253
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P97253
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LIGHT HARVESTING COMPLEX II	B, D [auth E], F [auth H], H [auth K]	45	Magnetospirillum molischianum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P95673 (Magnetospirillum molischianum) Explore P95673 Go to UniProtKB: P95673
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P95673
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCL Query on BCL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth G] SDF format, chain O [auth B] SDF format, chain U [auth D] SDF format, chain VA [auth J] SDF format, chain DB [auth K] SDF format, chain EA [auth E] SDF format, chain KA [auth G] SDF format, chain PA [auth H] SDF format, chain V [auth D] SDF format, chain WA [auth J] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain U [auth D] MOL2 format, chain VA [auth J] MOL2 format, chain DB [auth K] MOL2 format, chain EA [auth E] MOL2 format, chain KA [auth G] MOL2 format, chain PA [auth H] MOL2 format, chain V [auth D] MOL2 format, chain WA [auth J]	DB [auth K] EA [auth E] I [auth A] J [auth A] JA [auth G] DB [auth K], EA [auth E], I [auth A], J [auth A], JA [auth G], KA [auth G], O [auth B], PA [auth H], U [auth D], V [auth D], VA [auth J], WA [auth J]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain DB [auth K] Focus chain EA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain O [auth B] Focus chain PA [auth H] Focus chain U [auth D] Focus chain V [auth D] Focus chain VA [auth J] Focus chain WA [auth J]
LYC Query on LYC Download Ideal Coordinates CCD File SDF format, chain LA [auth G] SDF format, chain W [auth D] SDF format, chain K [auth A] SDF format, chain XA [auth J] MOL2 format, chain LA [auth G] MOL2 format, chain W [auth D] MOL2 format, chain K [auth A] MOL2 format, chain XA [auth J]	K [auth A], LA [auth G], W [auth D], XA [auth J]	LYCOPENE C₄₀ H₅₆ OAIJSZIZWZSQBC-GYZMGTAESA-N		Interactions Focus chain K [auth A] Focus chain LA [auth G] Focus chain W [auth D] Focus chain XA [auth J]
DET Query on DET Download Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain FB [auth K] SDF format, chain MA [auth G] SDF format, chain P [auth B] SDF format, chain X [auth D] SDF format, chain YA [auth J] SDF format, chain EB [auth K] SDF format, chain GA [auth E] SDF format, chain L [auth A] SDF format, chain Q [auth B] SDF format, chain QA [auth H] SDF format, chain RA [auth H] MOL2 format, chain FA [auth E] MOL2 format, chain FB [auth K] MOL2 format, chain MA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain X [auth D] MOL2 format, chain YA [auth J] MOL2 format, chain EB [auth K] MOL2 format, chain GA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth H] MOL2 format, chain RA [auth H]	EB [auth K] FA [auth E] FB [auth K] GA [auth E] L [auth A] EB [auth K], FA [auth E], FB [auth K], GA [auth E], L [auth A], MA [auth G], P [auth B], Q [auth B], QA [auth H], RA [auth H], X [auth D], YA [auth J]	UNDECYLAMINE-N,N-DIMETHYL-N-OXIDE C₁₃ H₂₉ N O OZHBUVQCJMARBN-UHFFFAOYSA-N		Interactions Focus chain EB [auth K] Focus chain FA [auth E] Focus chain FB [auth K] Focus chain GA [auth E] Focus chain L [auth A] Focus chain MA [auth G] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth H] Focus chain RA [auth H] Focus chain X [auth D] Focus chain YA [auth J]
HTO Query on HTO Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain BB [auth J] SDF format, chain CA [auth D] SDF format, chain DA [auth E] SDF format, chain M [auth A] SDF format, chain NA [auth G] SDF format, chain R [auth B] SDF format, chain S [auth D] SDF format, chain TA [auth J] SDF format, chain UA [auth J] SDF format, chain Y [auth D] SDF format, chain AB [auth J] SDF format, chain CB [auth K] SDF format, chain GB [auth K] SDF format, chain HA [auth E] SDF format, chain HB [auth K] SDF format, chain IA [auth E] SDF format, chain N [auth A] SDF format, chain OA [auth G] SDF format, chain SA [auth H] SDF format, chain T [auth D] SDF format, chain Z [auth D] SDF format, chain ZA [auth J] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain BB [auth J] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain S [auth D] MOL2 format, chain TA [auth J] MOL2 format, chain UA [auth J] MOL2 format, chain Y [auth D] MOL2 format, chain AB [auth J] MOL2 format, chain CB [auth K] MOL2 format, chain GB [auth K] MOL2 format, chain HA [auth E] MOL2 format, chain HB [auth K] MOL2 format, chain IA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth G] MOL2 format, chain SA [auth H] MOL2 format, chain T [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain ZA [auth J]	AA [auth D] AB [auth J] BA [auth D] BB [auth J] CA [auth D] AA [auth D], AB [auth J], BA [auth D], BB [auth J], CA [auth D], CB [auth K], DA [auth E], GB [auth K], HA [auth E], HB [auth K], IA [auth E], M [auth A], N [auth A], NA [auth G], OA [auth G], R [auth B], S [auth D], SA [auth H], T [auth D], TA [auth J], UA [auth J], Y [auth D], Z [auth D], ZA [auth J]	HEPTANE-1,2,3-TRIOL C₇ H₁₆ O₃ HXYCHJFUBNTKQR-RNFRBKRXSA-N		Interactions Focus chain AA [auth D] Focus chain AB [auth J] Focus chain BA [auth D] Focus chain BB [auth J] Focus chain CA [auth D] Focus chain CB [auth K] Focus chain DA [auth E] Focus chain GB [auth K] Focus chain HA [auth E] Focus chain HB [auth K] Focus chain IA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain R [auth B] Focus chain S [auth D] Focus chain SA [auth H] Focus chain T [auth D] Focus chain TA [auth J] Focus chain UA [auth J] Focus chain Y [auth D] Focus chain Z [auth D] Focus chain ZA [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.232
R-Value Work: 0.211
R-Value Observed: 0.211
Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.6	α = 90
b = 91.6	β = 90
c = 209.97	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 1997-06-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1997-06-05
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2024-04-03
Changes: Data collection, Database references, Derived calculations, Other, Refinement description