2P8J | pdb_00002p8j

Crystal structure of S-adenosylmethionine-dependent methyltransferase (NP_349143.1) from Clostridium acetobutylicum at 2.00 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2P8J/pdb

• Classification: TRANSFERASE
• Organism(s): Clostridium acetobutylicum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-03-22 Released: 2007-04-24 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Crystal structure of S-adenosylmethionine-dependent methyltransferase (NP_349143.1) from Clostridium acetobutylicum at 2.00 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)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 50.22 kDa 
• Atom Count: 3,761 
• Modeled Residue Count: 413 
• Deposited Residue Count: 418 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine-dependent methyltransferase	A, B	209	Clostridium acetobutylicum	Mutation(s): 4  Gene Names: NP_349143.1, CA_C2531
UniProt
Find proteins for Q97G40 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)) Explore Q97G40  Go to UniProtKB:  Q97G40

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	I [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	E [auth A], J [auth B], K [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 2.00 Å
• R-Value Free:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32P8J

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.86	α = 90
b = 83.86	β = 90
c = 159.2	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-24 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-04-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.6: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary