4LZH | pdb_00004lzh

L,D-transpeptidase from Klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb4LZH/pdb

• Classification: TRANSFERASE
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-07-31 Released: 2013-08-21 
• Deposition Author(s): Osipiuk, J., Hatzos-Skintges, C., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.179 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Literature

L,D-transpeptidase from Klebsiella pneumoniae.

Osipiuk, J., Hatzos-Skintges, C., Endres, M., Joachimiak, A.

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: 31.33 kDa 
• Atom Count: 2,425 
• Modeled Residue Count: 278 
• Deposited Residue Count: 285 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L,D-transpeptidase	A	285	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0  Gene Names: KPN78578_08240, KPN_00849, ybiS
UniProt
Find proteins for A6T6R4 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6T6R4  Go to UniProtKB:  A6T6R4

Small Molecules

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: 1.90 Å
• R-Value Free:  0.179 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34LZH

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.746	α = 90
b = 150.746	β = 90
c = 43.067	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-2000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-21 
Deposition Author(s): Osipiuk, J., Hatzos-Skintges, C., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-08-21
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary