3LPM | pdb_00003lpm

Crystal structure of putative methyltransferase small domain protein from Listeria monocytogenes

• PDB DOI: https://doi.org/10.2210/pdb3LPM/pdb

• Classification: TRANSFERASE
• Organism(s): Listeria monocytogenes serotype 4b str. CLIP 80459
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-02-05 Released: 2010-02-23 
• Deposition Author(s): Malashkevich, V.N., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.271 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Crystal structure of putative methyltransferase small domain protein from Listeria monocytogenes

Malashkevich, V.N., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 59.65 kDa 
• Atom Count: 3,675 
• Modeled Residue Count: 444 
• Deposited Residue Count: 518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative methyltransferase	A, B	259	Listeria monocytogenes serotype 4b str. CLIP 80459	Mutation(s): 0  Gene Names: CAC98380.1, Lm4b_00166

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.271 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.25	α = 90
b = 76.277	β = 90
c = 143.409	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-23 
Deposition Author(s): Malashkevich, V.N., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-11-06
  Changes: Data collection, Database references, Structure summary