4LPQ | pdb_00004lpq

Crystal structure of the L,D-transpeptidase (residues 123-326) from Xylanimonas cellulosilytica DSM 15894

• PDB DOI: https://doi.org/10.2210/pdb4LPQ/pdb

• Classification: TRANSFERASE
• Organism(s): Xylanimonas cellulosilytica DSM 15894
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-07-16 Released: 2013-11-13 
• Deposition Author(s): Nocek, B., Bigelow, L., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 
  0.146 (Depositor), 0.154 (DCC) 
• R-Value Work: 
  0.122 (Depositor), 0.133 (DCC) 
• R-Value Observed: 
  0.123 (Depositor) 

Literature

Crystal structure of the L,D-transpeptidase (residues 123-326) from Xylanimonas cellulosilytica DSM 15894

Nocek, B., Bigelow, L., Endres, M., Babnigg, G., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.17 kDa 
• Atom Count: 1,887 
• Modeled Residue Count: 204 
• Deposited Residue Count: 207 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ErfK/YbiS/YcfS/YnhG family protein	A	207	Xylanimonas cellulosilytica DSM 15894	Mutation(s): 0  Gene Names: Xcel_0604
UniProt
Find proteins for D1BWR1 (Xylanimonas cellulosilytica (strain DSM 15894 / JCM 12276 / CECT 5975 / KCTC 9989 / LMG 20990 / NBRC 107835 / XIL07)) Explore D1BWR1  Go to UniProtKB:  D1BWR1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A], C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.37 Å
• R-Value Free:  0.146 (Depositor), 0.154 (DCC) 
• R-Value Work:  0.122 (Depositor), 0.133 (DCC) 
• R-Value Observed: 0.123 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.849	α = 90
b = 62.849	β = 90
c = 167.21	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
ARP/wARP	model building
CCP$	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-13 
Deposition Author(s): Nocek, B., Bigelow, L., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-11-13
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary