3IBZ | pdb_00003ibz

Crystal structure of putative tellurium resistant like protein (TerD) from Streptomyces coelicolor A3(2)

• PDB DOI: https://doi.org/10.2210/pdb3IBZ/pdb

• Classification: structural genomics, unknown function
• Organism(s): Streptomyces coelicolor A3(2)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-07-17 Released: 2009-08-18 
• Deposition Author(s): Klimecka, M., Chruszcz, M., Cymborowski, M., Xu, X., Cui, H., Joachimiak, A., Edwards, A., Savchenko, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.200 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Crystal structure of putative tellurium resistant like protein (TerD) from Streptomyces coelicolor A3(2)

Klimecka, M., Chruszcz, M., Cymborowski, M., Xu, X., Cui, H., Joachimiak, A., Edwards, A., Savchenko, A., Minor, W.

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: 20.87 kDa 
• Atom Count: 1,549 
• Modeled Residue Count: 177 
• Deposited Residue Count: 191 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative tellurium resistant like protein TerD	A	191	Streptomyces coelicolor A3(2)	Mutation(s): 0  Gene Names: SCC8A.26c, SCO2368
UniProt
Find proteins for Q9KY22 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9KY22  Go to UniProtKB:  Q9KY22

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 1.78 Å
• R-Value Free:  0.200 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.836	α = 90
b = 61.456	β = 90
c = 85.713	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
ARP	model building
Coot	model building
CCP4	model building
SHELXE	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-18 
Deposition Author(s): Klimecka, M., Chruszcz, M., Cymborowski, M., Xu, X., Cui, H., Joachimiak, A., Edwards, A., Savchenko, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Advisory, Refinement description
• Version 1.3: 2022-04-13
  Changes: Advisory, Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-27
  Changes: Data collection, Structure summary