6FTL

Rubisco from Skeletonema marinoi

  • Classification: LYASE

  • Deposited: 2018-02-22 Released: 2018-06-27 
  • Deposition Author(s): Andersson, I., Valegard, K.
  • Funding Organization(s): European Union; Formas 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and functional analyses of Rubisco from arctic diatom species reveal unusual posttranslational modifications.

Valegard, K.Andralojc, P.J.Haslam, R.P.Pearce, F.G.Eriksen, G.K.Madgwick, P.J.Kristoffersen, A.K.van Lun, M.Klein, U.Eilertsen, H.C.Parry, M.A.J.Andersson, I.

(2018) J. Biol. Chem. 293: 13033-13043


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribulose bisphosphate carboxylase large chain
A, C, E, G
484N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
I, J, K, L
139N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
C, E, G, I, J, K, L
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C, E, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CAP
Query on CAP

Download SDF File 
Download CCD File 
A, C, E, G
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
 Ligand Interaction
Modified Residues  6 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
A, C, E, G
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
KCX
Query on KCX
A, C, E, G
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
HYP
Query on HYP
A, C, E, G
L-PEPTIDE LINKINGC5 H9 N O3PRO
LYO
Query on LYO
A, C, E, G
L-PEPTIDE LINKINGC6 H14 N2 O3

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LOH
Query on LOH
A, C, E, G
NON-POLYMERC6 H14 N2 O4

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HLU
Query on HLU
A, C, E, G
L-PEPTIDE LINKINGC6 H13 N O3LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.171 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 111.022α = 90.00
b = 111.022β = 90.00
c = 396.361γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European UnionSwedenQLK3-CT-2002-01945
FormasSweden--

Revision History 

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-07-04
    Type: Data collection, Database references
  • Version 1.2: 2018-09-05
    Type: Data collection, Database references
  • Version 1.3: 2019-04-17
    Type: Data collection, Structure summary