2RC3

Crystal structure of CBS domain, NE2398

• PDB DOI: https://doi.org/10.2210/pdb2RC3/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Nitrosomonas europaea ATCC 19718
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-09-19 Released: 2007-10-02 
• Deposition Author(s): Dong, A., Xu, X., Korniyenko, Y., Yakunin, A., Zheng, H., Walker, J.R., Edwards, A.M., Joachimiak, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.236 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 

Literature

Crystal structure of CBS domain, NE2398.

Dong, A., Xu, X., Korniyenko, A., Yakunin, A., Zheng, H., Walker, J.R., Edwards, A.M., Joachimiak, A., Savchenko, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.45 kDa 
• Atom Count: 4,859 
• Modelled Residue Count: 509 
• Deposited Residue Count: 540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CBS domain	A, B, C, D	135	Nitrosomonas europaea ATCC 19718	Mutation(s): 0  Gene Names: NE2398
UniProt
Find proteins for Q82SE2 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Go to UniProtKB:  Q82SE2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	GA [auth C], M [auth A], S [auth B], UA [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
BR	AA [auth C], BA [auth C], CA [auth C], DA [auth C], E [auth A], EA [auth C], F [auth A], FA [auth C], G [auth A], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], MA [auth D], N [auth B], NA [auth D], O [auth B], OA [auth D], P [auth B], PA [auth D], Q [auth B], QA [auth D], R [auth B], RA [auth D], SA [auth D], T [auth C], TA [auth D], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.236 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.195	α = 90
b = 95.641	β = 90
c = 99.759	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-02 
Deposition Author(s): Dong, A., Xu, X., Korniyenko, Y., Yakunin, A., Zheng, H., Walker, J.R., Edwards, A.M., Joachimiak, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-10-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations