3NWR | pdb_00003nwr

Crystal structure of a rubisco-like protein from Burkholderia fungorum

• PDB DOI: https://doi.org/10.2210/pdb3NWR/pdb

• Classification: LYASE
• Organism(s): Paraburkholderia fungorum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-10 Released: 2010-07-28 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Imker, H.J., Gerlt, J.A., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.188 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Crystal structure of a rubisco-like protein from Burkholderia fungorum

Fedorov, A.A., Fedorov, E.V., Imker, H.J., Gerlt, J.A., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 47.4 kDa 
• Atom Count: 3,398 
• Modeled Residue Count: 404 
• Deposited Residue Count: 432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A rubisco-like protein	A	432	Paraburkholderia fungorum	Mutation(s): 0
UniProt
Find proteins for D9N172 (Paraburkholderia fungorum) Explore D9N172  Go to UniProtKB:  D9N172

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.188 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.255	α = 90
b = 130.917	β = 90
c = 101.452	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-28 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Imker, H.J., Gerlt, J.A., Almo, S.C.

Revision History  

• Version 1.0: 2010-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary