3E8S | pdb_00003e8s

Crystal structure of Putative SAM Dependent Methyltransferase in Complex with SAH (NP_744700.1) from PSEUDOMONAS PUTIDA KT2440 at 2.10 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3E8S/pdb

• Classification: TRANSFERASE
• Organism(s): Pseudomonas putida KT2440
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-20 Released: 2008-09-02 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.176 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Literature

Crystal structure of Putative SAM Dependent Methyltransferase in Complex with SAH (NP_744700.1) from PSEUDOMONAS PUTIDA KT2440 at 2.10 A resolution

Joint Center for Structural Genomics (JCSG)

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: 25.62 kDa 
• Atom Count: 2,000 
• Modeled Residue Count: 220 
• Deposited Residue Count: 227 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative SAM Dependent Methyltransferase	A	227	Pseudomonas putida KT2440	Mutation(s): 0  Gene Names: NP_744700.1, PP2555, PP_2555
UniProt
Find proteins for Q88JU2 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88JU2  Go to UniProtKB:  Q88JU2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-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: 2.10 Å
• R-Value Free:  0.176 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33E8S

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.433	α = 90
b = 130.433	β = 90
c = 54.431	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
autoSHARP	phasing
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-02 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-09-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Structure summary