3KLU | pdb_00003klu

Crystal structure of the protein yqbn. northeast structural genomics consortium target sr445.

• PDB DOI: https://doi.org/10.2210/pdb3KLU/pdb
• Entry: 3KLU supersedes: 3DFD

• Classification: structural genomics, unknown function
• Organism(s): Bacillus subtilis
• Mutation(s): No 


• Deposited: 2009-11-09 Released: 2009-11-24 
• Deposition Author(s): Kuzin, A.P., Su, M., Seetharaman, J., Wang, D., Fang, Y., Cunningham, K., Ma, L.-C., Xiao, R., Liu, M., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.246 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.242 (DCC) 

Literature

Crystal structure of the protein yqbn. northeast structural genomics consortium target sr445.

Kuzin, A.P., Su, M., Seetharaman, J., Wang, D., Fang, Y., Cunningham, K., Ma, L.-C., Xiao, R., Liu, M., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 18.38 kDa 
• Atom Count: 993 
• Modeled Residue Count: 119 
• Deposited Residue Count: 157 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein yqbN	A	157	Bacillus subtilis	Mutation(s): 0  Gene Names: yqbN, BSU26040
UniProt
Find proteins for P45930 (Bacillus subtilis (strain 168)) Explore P45930  Go to UniProtKB:  P45930

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.246 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.242 (DCC) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.101	α = 90
b = 70.101	β = 90
c = 59.161	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-24 
Deposition Author(s): Kuzin, A.P., Su, M., Seetharaman, J., Wang, D., Fang, Y., Cunningham, K., Ma, L.-C., Xiao, R., Liu, M., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)
• This entry supersedes: 3DFD

Revision History  

• Version 1.0: 2009-11-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary