1NE8 | pdb_00001ne8

YDCE protein from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb1NE8/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-12-10 Released: 2003-01-14 
• Deposition Author(s): Gogos, A., Mu, H., Bahna, F., Gomez, C.A., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.210 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Literature

Crystal structure of YdcE protein from Bacillus subtilis

Gogos, A., Mu, H., Bahna, F., Gomez, C.A., Shapiro, L.

(2003) Proteins 53: 320-322

• PubMed: 14517982 
• DOI: https://doi.org/10.1002/prot.10457
• Primary Citation Related Structures: 
  1NE8

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biophysics, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.69 kDa 
• Atom Count: 1,036 
• Modeled Residue Count: 116 
• Deposited Residue Count: 117 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
conserved hypothetical protein YDCE	A	117	Bacillus subtilis	Mutation(s): 0  Gene Names: ydcE EC: 3.1.27
UniProt
Find proteins for P96622 (Bacillus subtilis (strain 168)) Explore P96622  Go to UniProtKB:  P96622

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PG	B [auth A], C [auth A]	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C11 H24 O6 SLNYBUIEAMRFSZ-UHFFFAOYSA-N
ACY	D [auth A], E [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.210 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.63	α = 90
b = 56.63	β = 90
c = 138.257	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-01-14 
Deposition Author(s): Gogos, A., Mu, H., Bahna, F., Gomez, C.A., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2003-01-14
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references