4HYL | pdb_00004hyl

The crystal structure of an anti-sigma-factor antagonist from Haliangium ochraceum DSM 14365

• PDB DOI: https://doi.org/10.2210/pdb4HYL/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Haliangium ochraceum DSM 14365
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-11-13 Released: 2012-11-28 
• Deposition Author(s): Tan, K., Chhor, G., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.229 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

The crystal structure of an anti-sigma-factor antagonist from Haliangium ochraceum DSM 14365

Tan, K., Chhor, G., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 26.5 kDa 
• Atom Count: 1,891 
• Modeled Residue Count: 228 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stage II sporulation protein	A, B	117	Haliangium ochraceum DSM 14365	Mutation(s): 0  Gene Names: Haliangium ochraceum, Hoch_4443
UniProt
Find proteins for D0LNN2 (Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2)) Explore D0LNN2  Go to UniProtKB:  D0LNN2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], E [auth A], F [auth A], I [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.229 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.466	α = 90
b = 59.466	β = 90
c = 65.599	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-28 
Deposition Author(s): Tan, K., Chhor, G., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-11-28
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary