5BMQ | pdb_00005bmq

Crystal structure of L,D-transpeptidase (Yku) from Stackebrandtia nassauensis

• PDB DOI: https://doi.org/10.2210/pdb5BMQ/pdb

• Classification: HYDROLASE
• Organism(s): Stackebrandtia nassauensis DSM 44728
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-05-22 Released: 2015-06-03 
• Deposition Author(s): Chang, C., Bigelow, L., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.178 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Literature

Crystal structures of L,D-transpeptidases (Yku)

Chang, C., Bigelow, L., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.41 kDa 
• Atom Count: 1,919 
• Modeled Residue Count: 205 
• Deposited Residue Count: 243 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ErfK/YbiS/YcfS/YnhG family protein	A	243	Stackebrandtia nassauensis DSM 44728	Mutation(s): 0  Gene Names: Snas_6095 EC: 3
UniProt
Find proteins for D3Q1D9 (Stackebrandtia nassauensis (strain DSM 44728 / CIP 108903 / NRRL B-16338 / NBRC 102104 / LLR-40K-21)) Explore D3Q1D9  Go to UniProtKB:  D3Q1D9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DIO	C [auth A]	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-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: 2.05 Å
• R-Value Free:  0.178 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.356	α = 90
b = 143.356	β = 90
c = 143.356	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing
SBC-Collect	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-03 
Deposition Author(s): Chang, C., Bigelow, L., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2015-06-03
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary