4R4G

Crystal structure of a putative lipoprotein (ycdA) from Bacillus subtilis subsp. subtilis str. 168 at 2.62 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4R4G/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-19 Released: 2014-09-17 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 0.239 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 

Literature

Crystal structure of a putative lipoprotein (ycdA) from Bacillus subtilis subsp. subtilis str. 168 at 2.62 A resolution

Joint Center for Structural Genomics (JCSG)

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: 36.87 kDa 
• Atom Count: 2,584 
• Modelled Residue Count: 322 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative lipoprotein YcdA	A	326	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: ycdA, BSU02780
UniProt
Find proteins for O34538 (Bacillus subtilis (strain 168)) Explore O34538  Go to UniProtKB:  O34538

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	B [auth A], C [auth A], D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-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: 2.62 Å
• R-Value Free: 0.239 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 
• Space Group: P 6₅ 2 2
• Diffraction Data: https://doi.org/10.18430/M34R4G

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.653	α = 90
b = 98.653	β = 90
c = 195.018	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations