Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 25.12 kDa 
• Atom Count: 1426 
• Modelled Residue Count: 179 
• Deposited Residue Count: 226 
• Unique protein chains: 1

2PZ9

Crystal structure of putative transcriptional regulator SCO4942 from Streptomyces coelicolor

• PDB DOI: 10.2210/pdb2PZ9/pdb

• Classification: TRANSCRIPTION
• Organism(s): Streptomyces coelicolor A3(2)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-05-17 Released: 2007-06-19 
• Deposition Author(s): Filippova, E.V., Chruszcz, M., Xu, X., Zheng, H., Cymborowski, M., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.269 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 

Literature

In situ proteolysis for protein crystallization and structure determination.

Dong, A., Xu, X., Edwards, A.M., Chang, C., Chruszcz, M., Cuff, M., Cymborowski, M., Di Leo, R., Egorova, O., Evdokimova, E., Filippova, E., Gu, J., Guthrie, J., Ignatchenko, A., Joachimiak, A., Klostermann, N., Kim, Y., Korniyenko, Y., Minor, W., Que, Q., Savchenko, A., Skarina, T., Tan, K., Yakunin, A., Yee, A., Yim, V., Zhang, R., Zheng, H., Akutsu, M., Arrowsmith, C., Avvakumov, G.V., Bochkarev, A., Dahlgren, L.G., Dhe-Paganon, S., Dimov, S., Dombrovski, L., Finerty, P., Flodin, S., Flores, A., Graslund, S., Hammerstrom, M., Herman, M.D., Hong, B.S., Hui, R., Johansson, I., Liu, Y., Nilsson, M., Nedyalkova, L., Nordlund, P., Nyman, T., Min, J., Ouyang, H., Park, H.W., Qi, C., Rabeh, W., Shen, L., Shen, Y., Sukumard, D., Tempel, W., Tong, Y., Tresagues, L., Vedadi, M., Walker, J.R., Weigelt, J., Welin, M., Wu, H., Xiao, T., Zeng, H., Zhu, H.

(2007) Nat Methods 4: 1019-1021

• PubMed: 17982461 
• DOI: 10.1038/nmeth1118
• Primary Citation of Related Structures:  
  2PZ9


• PubMed Abstract: 
  

We tested the general applicability of in situ proteolysis to form protein crystals suitable for structure determination by adding a protease (chymotrypsin or trypsin) digestion step to crystallization trials of 55 bacterial and 14 human proteins that had proven recalcitrant to our best efforts at crystallization or structure determination. This is a work in progress; so far we determined structures of 9 bacterial proteins and the human aminoimidazole ribonucleotide synthetase (AIRS) domain.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Toronto, 100 College Street, Toronto, Ontario M5G 1L5, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative regulatory protein	A	226	Streptomyces coelicolor A3(2)	Mutation(s): 0  Gene Names: SCO4942, 2SCK31.02c
UniProt
Find proteins for Q9EWE9 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9EWE9  Go to UniProtKB:  Q9EWE9

Small Molecules

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

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: 2.80 Å
• R-Value Free: 0.269 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.96	α = 90
b = 66.96	β = 90
c = 104.345	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
O	model building
SOLVE	phasing
SHELXE	model building
RESOLVE	model building
Coot	model building
CCP4	model building
REFMAC	refinement
ADSC	data collection
HKL-2000	data scaling
DM	phasing
RESOLVE	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-05-17 
• Released Date: 2007-06-19 
Deposition Author(s): Filippova, E.V., Chruszcz, M., Xu, X., Zheng, H., Cymborowski, M., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-06-19
  Type: Initial release
  
• Version 1.1: 2007-11-14
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary