5BMO | pdb_00005bmo

LnmX protein, a putative GlcNAc-PI de-N-acetylase from Streptomyces atroolivaceus

• PDB DOI: https://doi.org/10.2210/pdb5BMO/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces atroolivaceus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-22 Released: 2015-06-10 
• Deposition Author(s): Osipiuk, J., Hatzos-Skintges, C., Cuff, M., Endres, M., Babnigg, G., Lohman, J., Ma, M., Rudolf, J., Chang, C.-Y., Shen, B., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.168 (Depositor) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

LnmX protein, a putative GlcNAc-PI de-N-acetylase from Streptomyces atroolivaceus.

Osipiuk, J., Hatzos-Skintges, C., Cuff, M., Endres, M., Babnigg, G., Lohman, J., Ma, M., Rudolf, J., Chang, C.-Y., Shen, B., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 80.31 kDa 
• Atom Count: 5,916 
• Modeled Residue Count: 723 
• Deposited Residue Count: 738 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein LnmX	A, B, C	246	Streptomyces atroolivaceus	Mutation(s): 0  Gene Names: LnmX
UniProt
Find proteins for Q8GGM8 (Streptomyces atroolivaceus) Explore Q8GGM8  Go to UniProtKB:  Q8GGM8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	E [auth A], G [auth B], I [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
K	D [auth A], F [auth B], H [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.168 (Depositor) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.998	α = 90
b = 71.998	β = 90
c = 284.458	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-06-10 
Deposition Author(s): Osipiuk, J., Hatzos-Skintges, C., Cuff, M., Endres, M., Babnigg, G., Lohman, J., Ma, M., Rudolf, J., Chang, C.-Y., Shen, B., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094585

Revision History  

• Version 1.0: 2015-06-10
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description