3A13

Crystal structure of Type III Rubisco SP4 mutant complexed with 2-CABP and activated with Ca


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Structure-based optimization of a Type III Rubisco from a hyperthermophile

Nishitani, Y.Fujihashi, M.Doi, T.Yoshida, S.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): 5 
Gene Names: rbcLTK2290
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 
BA [auth I]
DA [auth J]
L [auth A]
N [auth B]
P [auth C]
BA [auth I],
DA [auth J],
L [auth A],
N [auth B],
P [auth C],
R [auth D],
T [auth E],
V [auth F],
X [auth G],
Z [auth H]
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
CA [auth J],
S [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth I]
K [auth A]
M [auth B]
O [auth C]
Q [auth D]
AA [auth I],
K [auth A],
M [auth B],
O [auth C],
Q [auth D],
U [auth F],
W [auth G],
Y [auth H]
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: 2.34 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.678α = 90
b = 247.09β = 90
c = 144.94γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-09-09
    Changes: Database references, Derived calculations
  • Version 1.3: 2021-11-10
    Changes: Database references
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-11-15
    Changes: Data collection