1GK8

Rubisco from Chlamydomonas reinhardtii

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.149 

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Literature

First Crystal Structure of Rubisco from a Green Alga, Chlamydomonas Reinhardtii.

Taylor, T.C., Backlund, A., Bjorhall, K., Spreitzer, R.J., Andersson, I.

(2001) J Biol Chem 276: 48159

  • DOI: https://doi.org/10.1074/jbc.M107765200
  • Primary Citation of Related Structures:  
    1GK8

  • PubMed Abstract: 

    • The crystal structure of Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase) from the unicellular green alga Chlamydomonas reinhardtii has been determined to 1.4 A resolution. Overall, the structure shows high similarity to the previously determined structures of L8S8 Rubisco enzymes ...

    The crystal structure of Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase) from the unicellular green alga Chlamydomonas reinhardtii has been determined to 1.4 A resolution. Overall, the structure shows high similarity to the previously determined structures of L8S8 Rubisco enzymes. The largest difference is found in the loop between beta strands A and B of the small subunit (betaA-betaB loop), which is longer by six amino acid residues than the corresponding region in Rubisco from Spinacia. Mutations of residues in the betaA-betaB loop have been shown to affect holoenzyme stability and catalytic properties. The information contained in the Chlamydomonas structure enables a more reliable analysis of the effect of these mutations. No electron density was observed for the last 13 residues of the small subunit, which are assumed to be disordered in the crystal. Because of the high resolution of the data, some posttranslational modifications are unambiguously apparent in the structure. These include cysteine and N-terminal methylations and proline 4-hydroxylations.

    Organizational Affiliation: 

    Department of Molecular Biology, Swedish University of Agricultural Sciences, BMC Box 590, S-751 24 Uppsala, Sweden.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBULOSE-1,5 BISPHOSPHATE CARBOXYLASE LARGE CHAINA,
B [auth C],
C [auth E],
D [auth G]		475Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: rbcL
EC: 4.1.1.39
UniProt
Find proteins for P00877 (Chlamydomonas reinhardtii)
Explore P00877 
Go to UniProtKB:  P00877
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00877
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1E [auth I],
F [auth K],
G [auth M],
H [auth O]		140Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: RBCS1, RBCS-1, CHLRE_02g120100v5, CHLREDRAFT_82986
EC: 4.1.1.39
UniProt
Find proteins for P00873 (Chlamydomonas reinhardtii)
Explore P00873 
Go to UniProtKB:  P00873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00873
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAP
Query on CAP
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IA [auth G],
J [auth A],
S [auth C],
Z [auth E]		2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N		 Ligand Interaction
EDO
Query on EDO
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AA [auth E]
BA [auth E]
CA [auth E]
DA [auth E]
EA [auth E]
AA [auth E],
BA [auth E],
CA [auth E],
DA [auth E],
EA [auth E],
FA [auth E],
GA [auth E],
JA [auth G],
K [auth A],
KA [auth G],
L [auth A],
LA [auth G],
M [auth A],
MA [auth G],
N [auth A],
NA [auth G],
O [auth A],
OA [auth G],
P [auth A],
PA [auth I],
Q [auth A],
QA [auth I],
RA [auth K],
SA [auth K],
T [auth C],
TA [auth M],
U [auth C],
UA [auth M],
V [auth C],
VA [auth O],
W [auth C],
WA [auth O],
X [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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HA [auth G],
I [auth A],
R [auth C],
Y [auth E]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP		A,
B [auth C],
C [auth E],
D [auth G]		L-PEPTIDE LINKINGC5 H9 N O3PRO
KCX
Query on KCX		A,
B [auth C],
C [auth E],
D [auth G]		L-PEPTIDE LINKINGC7 H14 N2 O4LYS
SMC
Query on SMC		A,
B [auth C],
C [auth E],
D [auth G]		L-PEPTIDE LINKINGC4 H9 N O2 SCYS
MME
Query on MME		E [auth I],
F [auth K],
G [auth M],
H [auth O]		L-PEPTIDE LINKINGC6 H13 N O2 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.149 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.375α = 90
b = 142.638β = 124.13
c = 124.717γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2001-10-24 
    • Deposition Author(s): Taylor, T.C.

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-24
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other