1SVD | pdb_00001svd

The structure of Halothiobacillus neapolitanus RuBisCo

• PDB DOI: https://doi.org/10.2210/pdb1SVD/pdb

• Classification: LYASE
• Organism(s): Halothiobacillus neapolitanus
• Mutation(s): No 


• Deposited: 2004-03-29 Released: 2005-04-12 
• Deposition Author(s): Kerfeld, C.A., Sawaya, M.R., Pashkov, I., Cannon, G., Williams, E., Tran, K., Yeates, T.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.166 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Starting Model: experimental

Literature

The structure of Halothiobacillus neapolitanus RuBisCo

Kerfeld, C.A., Sawaya, M.R., Pashkov, I., Cannon, G., Williams, E., Tran, K., Yeates, T.O.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Hetero 16-mer - A8B8 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 65.85 kDa 
• Atom Count: 4,778 
• Modeled Residue Count: 553 
• Deposited Residue Count: 583 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit	A	473	Halothiobacillus neapolitanus	Mutation(s): 0  EC: 4.1.1.39
UniProt
Find proteins for O85040 (Halothiobacillus neapolitanus (strain ATCC 23641 / c2)) Explore O85040  Go to UniProtKB:  O85040

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase small chain	B [auth M]	110	Halothiobacillus neapolitanus	Mutation(s): 0  EC: 4.1.1.39
UniProt
Find proteins for P45686 (Halothiobacillus neapolitanus (strain ATCC 23641 / c2)) Explore P45686  Go to UniProtKB:  P45686

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth M]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.166 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.066	α = 90
b = 157.066	β = 90
c = 107.609	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-12 
Deposition Author(s): Kerfeld, C.A., Sawaya, M.R., Pashkov, I., Cannon, G., Williams, E., Tran, K., Yeates, T.O.

Revision History  

• Version 1.0: 2005-04-12
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description