2O1E

Crystal Structure of the Metal-dependent Lipoprotein YcdH from Bacillus subtilis, Northeast Structural Genomics Target SR583

• PDB DOI: https://doi.org/10.2210/pdb2O1E/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-11-28 Released: 2006-12-12 
• Deposition Author(s): Forouhar, F., Zhou, W., Seetharaman, J., Chen, C.X., Fang, Y., Cunningham, K., Ma, L.-C., Janjua, H., Xiao, R., Baran, M.C., Liu, J., Acton, T.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: 2.60 Å
• R-Value Free: 0.290 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 

Literature

Crystal Structure of the Metal-dependent Lipoprotein YcdH from Bacillus subtilis, Northeast Structural Genomics Target SR583

Forouhar, F., Zhou, W., Seetharaman, J., Chen, C.X., Fang, Y., Cunningham, K., Ma, L.-C., Janjua, H., Xiao, R., Baran, M.C., Liu, J., Acton, T.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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 71.02 kDa 
• Atom Count: 4,236 
• Modelled Residue Count: 530 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YcdH	A, B	312	Bacillus subtilis	Mutation(s): 6  Gene Names: ycdH, locus_tag=BSU02850
UniProt
Find proteins for O34966 (Bacillus subtilis (strain 168)) Explore O34966  Go to UniProtKB:  O34966

Small Molecules

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.290 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.292	α = 103.7
b = 54.344	β = 100.46
c = 62.84	γ = 96.75

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-12 
Deposition Author(s): Forouhar, F., Zhou, W., Seetharaman, J., Chen, C.X., Fang, Y., Cunningham, K., Ma, L.-C., Janjua, H., Xiao, R., Baran, M.C., Liu, J., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2006-12-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-11-06
  Changes: Structure summary