1NKZ

Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution

Structural Biology Knowledgebase: 1NKZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.190
  • R-Value Work: 0.169

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1NKZ

Classification: MEMBRANE PROTEIN

Total Structure Weight: 45394.65

Macromolecule Entities
Molecule Chains Length Organism Details
Light-harvesting protein B-800/850, alpha chain A, C, E 53 Rhodoblastus acidophilus Mutation: M1X
Gene Name(s):
Light-harvesting protein B-800/850, beta chain B, D, F 41 Rhodoblastus acidophilus Gene Name(s):

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Light-Harvesting Complexes

Protein Name: Light Harvesting Complex


Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BCL
Query on BCL

A, B, C, D, E, F BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RG1
Query on RG1

A, B, C, D, E Rhodopin b-D-glucoside
(3E)-3,4-didehydro-1',2'-dihydro-psi,psi- caroten-1'-yl beta-D-glucopyranoside (Synonym)
C46 H66 O6
ISHBHDBCVQRMDY-GZIKAPSJSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BOG
Query on BOG

A, C, E B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BEN
Query on BEN

C, E BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CXM
Query on CXM
A, C, E L-PEPTIDE LINKING C6 H11 N O4 S MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.190
  • R-Value Work: 0.169
  • Space Group: H 3 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 117.05 α = 90.00
b = 117.05 β = 90.00
c = 298.44 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-01-06
  • Released Date: 2003-02-25
  • Deposition author(s): Papiz, M.Z., Prince, S.M., Howard, T, Cogdell, R.J., Isaacs, N.W.

Revision History

  • 2016-03-30
    Type: Non-polymer description | Details: --
  • 2014-04-16
    Type: Data collection | Details: --
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values