1SBK | pdb_00001sbk

X-RAY STRUCTURE OF YDII_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER29.

• PDB DOI: https://doi.org/10.2210/pdb1SBK/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-02-10 Released: 2004-02-24 
• Deposition Author(s): Kuzin, A.P., Edstrom, W., Vorobiev, S.M., Lee, I., Forouhar, F., Ma, L., Chiang, Y., Rong, X., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.272 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

X-ray Structure of YDII_ECOLI Northeast Structural Genomics Consortium Target ER29

Kuzin, A.P., Edstrom, W., Vorobiev, S.M., Lee, I., Forouhar, F., Ma, L., Chiang, Y., Rong, X., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 65.28 kDa 
• Atom Count: 4,693 
• Modeled Residue Count: 552 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ydiI	A, B, C, D	144	Escherichia coli	Mutation(s): 4  Gene Names: YDII, B1686 EC: 3.1.2.28
UniProt
Find proteins for P77781 (Escherichia coli (strain K12)) Explore P77781  Go to UniProtKB:  P77781

Small Molecules

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

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: 2.00 Å
• R-Value Free:  0.272 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.642	α = 90
b = 61.196	β = 104.66
c = 93.008	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-02-24 
Deposition Author(s): Kuzin, A.P., Edstrom, W., Vorobiev, S.M., Lee, I., Forouhar, F., Ma, L., Chiang, Y., Rong, X., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2004-02-24
  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: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-11-20
  Changes: Structure summary