2RJB | pdb_00002rjb

Crystal structure of uncharacterized protein YdcJ (SF1787) from Shigella flexneri which includes domain DUF1338. Northeast Structural Genomics Consortium target SfR276

• PDB DOI: https://doi.org/10.2210/pdb2RJB/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Shigella flexneri
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-10-14 Released: 2007-10-30 
• Deposition Author(s): Seetharaman, J., Chen, Y., Wang, D., Fang, Y., Cunningham, K., Ma, L.-C., Xia, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.281 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

Crystal structure of uncharacterized protein YdcJ (SF1787) from Shigella flexneri which includes domain DUF1338.

Seetharaman, J., Chen, Y., Wang, D., Fang, Y., Cunningham, K., Ma, L.-C., Xia, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 211.12 kDa 
• Atom Count: 13,227 
• Modeled Residue Count: 1,572 
• Deposited Residue Count: 1,820 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D	455	Shigella flexneri	Mutation(s): 0  Gene Names: S1487, SF1787 EC: 1.13.11.93
UniProt
Find proteins for A0A0H2UZX2 (Shigella flexneri) Explore A0A0H2UZX2  Go to UniProtKB:  A0A0H2UZX2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth B], G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	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:  0.281 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 192.209	α = 90
b = 76.387	β = 116.55
c = 159.052	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-30 
Deposition Author(s): Seetharaman, J., Chen, Y., Wang, D., Fang, Y., Cunningham, K., Ma, L.-C., Xia, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2007-10-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary