4OBM | pdb_00004obm

Crystal structure of a putative transcription regulator (EUBSIR_01389) from Eubacterium siraeum DSM 15702 at 2.15 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4OBM/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): [Eubacterium] siraeum DSM 15702
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-01-07 Released: 2014-02-12 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.245 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Crystal structure of a hypothetical protein (EUBSIR_01389) from Eubacterium siraeum DSM 15702 at 2.15 A resolution

Joint Center for Structural Genomics (JCSG)

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: 29.52 kDa 
• Atom Count: 2,206 
• Modeled Residue Count: 258 
• Deposited Residue Count: 259 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	259	[Eubacterium] siraeum DSM 15702	Mutation(s): 0  Gene Names: EUBSIR_01389, ZP_02422542.1
UniProt
Find proteins for B0MNI4 ([Eubacterium] siraeum DSM 15702) Explore B0MNI4  Go to UniProtKB:  B0MNI4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	C [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PG4	B [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-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: 2.15 Å
• R-Value Free:  0.245 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34OBM

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.503	α = 90
b = 51.466	β = 90
c = 104.712	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-12 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2014-02-12
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Structure summary
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary