3KVP

Crystal Structure of Uncharacterized protein ymzC Precursor from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR378A

• PDB DOI: https://doi.org/10.2210/pdb3KVP/pdb

• Classification: structural genomics, unknown function
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-11-30 Released: 2010-02-02 
• Deposition Author(s): Kuzin, A.P., Chen, Y., Seetharaman, J., Afonine, P., Fang, F., Xiao, R., Cunningham, K., Ma, L., Chen, C.X., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.237 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

Northeast Structural Genomics Consortium Target SR378A

Kuzin, A.P., Chen, Y., Afonine, P., Seetharaman, J., Fang, F., Xiao, R., Cunningham, K., Ma, L., Chen, C.X., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.17 kDa 
• Atom Count: 2,286 
• Modelled Residue Count: 265 
• Deposited Residue Count: 432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein ymzC	A, B, C, D, E, F	72	Bacillus subtilis	Mutation(s): 0  Gene Names: BSU17350, ymzC
UniProt
Find proteins for O31797 (Bacillus subtilis (strain 168)) Explore O31797  Go to UniProtKB:  O31797

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	G [auth B], H [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.237 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.39	α = 90
b = 66.39	β = 90
c = 175.573	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-02 
Deposition Author(s): Kuzin, A.P., Chen, Y., Seetharaman, J., Afonine, P., Fang, F., Xiao, R., Cunningham, K., Ma, L., Chen, C.X., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2010-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description