1YDM | pdb_00001ydm

X-Ray structure of Northeast Structural Genomics target SR44

• PDB DOI: https://doi.org/10.2210/pdb1YDM/pdb

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


• Deposited: 2004-12-24 Released: 2005-01-18 
• Deposition Author(s): Kuzin, A.P., Jianwei, S., Vorobiev, S., Acton, T., Xia, R., Ma, L.-C., Montelione, G., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.304 (Depositor), 0.305 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Literature

X-Ray structure of Northeast Structural Genomics target SR44

Kuzin, A.P., Jianwei, S., Vorobiev, S., Acton, T., Xia, R., Ma, L.-C., Montelione, G., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 65.03 kDa 
• Atom Count: 4,438 
• Modeled Residue Count: 542 
• Deposited Residue Count: 561 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein yqgN	A, B, C	187	Bacillus subtilis	Mutation(s): 3  Gene Names: yqgN
UniProt
Find proteins for P54491 (Bacillus subtilis (strain 168)) Explore P54491  Go to UniProtKB:  P54491

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth B], F [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.304 (Depositor), 0.305 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.302	α = 90
b = 44.276	β = 104.99
c = 85.296	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-18 
Deposition Author(s): Kuzin, A.P., Jianwei, S., Vorobiev, S., Acton, T., Xia, R., Ma, L.-C., Montelione, G., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2005-01-18
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary