3WQP

Crystal structure of Rubisco T289D mutant from Thermococcus kodakarensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Mutation design of thermophilic Rubisco based on the three-dimensional structure enhances its activity at ambient temperature

Kiriyama, T.Fujihashi, M.Nishitani, Y.Aono, R.Sato, T.Takai, T.Tagashira, K.Fukuda, W.Atomi, H.Imanaka, T.Miki, K.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
444Thermococcus kodakarensis KOD1Mutation(s): 1 
Gene Names: rbcLrbcTK2290
EC: 4.1.1.39
UniProt
Find proteins for O93627 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore O93627 
Go to UniProtKB:  O93627
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO93627
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CAP
Query on CAP

Download Ideal Coordinates CCD File 
AA [auth F]
CA [auth G]
EA [auth H]
IA [auth I]
L [auth A]
AA [auth F],
CA [auth G],
EA [auth H],
IA [auth I],
L [auth A],
MA [auth J],
O [auth B],
R [auth C],
U [auth D],
X [auth E]
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
FA [auth H]
GA [auth H]
JA [auth I]
KA [auth I]
M [auth A]
FA [auth H],
GA [auth H],
JA [auth I],
KA [auth I],
M [auth A],
NA [auth J],
P [auth B],
S [auth C],
V [auth D],
Y [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth G]
DA [auth H]
HA [auth I]
K [auth A]
LA [auth J]
BA [auth G],
DA [auth H],
HA [auth I],
K [auth A],
LA [auth J],
N [auth B],
Q [auth C],
T [auth D],
W [auth E],
Z [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.566α = 90
b = 246.238β = 90
c = 144.628γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2023-12-06
    Changes: Data collection