1SDI | pdb_00001sdi

1.65 A structure of Escherichia coli ycfC gene product

• PDB DOI: https://doi.org/10.2210/pdb1SDI/pdb

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


• Deposited: 2004-02-13 Released: 2004-08-03 
• Deposition Author(s): Borek, D., Otwinowski, Z., Chen, Y., Skarina, T., Savchenko, A., Edwards, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.184 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

Structural analysis of Escherichia coli ycfC gene product

Borek, D., Otwinowski, Z., Chen, Y., Skarina, T., Savchenko, A., Edwards, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.14 kDa 
• Atom Count: 1,858 
• Modeled Residue Count: 213 
• Deposited Residue Count: 213 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ycfC	A	213	Escherichia coli	Mutation(s): 0  Gene Names: YCFC, B1132
UniProt
Find proteins for P25746 (Escherichia coli (strain K12)) Explore P25746  Go to UniProtKB:  P25746

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACY	B [auth A], C [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.184 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.527	α = 90
b = 62.649	β = 90
c = 68.816	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-03 
Deposition Author(s): Borek, D., Otwinowski, Z., Chen, Y., Skarina, T., Savchenko, A., Edwards, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2004-08-03
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations