3DLC | pdb_00003dlc

Crystal structure of a putative s-adenosyl-l-methionine-dependent methyltransferase (mmp1179) from methanococcus maripaludis at 1.15 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3DLC/pdb

• Classification: TRANSFERASE
• Organism(s): Methanococcus maripaludis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-27 Released: 2008-08-26 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.138 (Depositor), 0.137 (DCC) 
• R-Value Work: 
  0.120 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.121 (Depositor) 

Literature

Crystal structure of a Putative S-adenosyl-L-methionine-dependent Methyltransferase (NP_988299.1) from Methanococcus maripaludis JJ (DSM 2067) at 1.15 A resolution

Joint Center for Structural Genomics (JCSG)

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: 25.4 kDa 
• Atom Count: 2,307 
• Modeled Residue Count: 219 
• Deposited Residue Count: 219 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative S-adenosyl-L-methionine-dependent Methyltransferase	A	219	Methanococcus maripaludis	Mutation(s): 0  Gene Names: NP_988299.1, MMP1179
UniProt
Find proteins for Q6LY14 (Methanococcus maripaludis (strain DSM 14266 / JCM 13030 / NBRC 101832 / S2 / LL)) Explore Q6LY14  Go to UniProtKB:  Q6LY14

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-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: 1.15 Å
• R-Value Free:  0.138 (Depositor), 0.137 (DCC) 
• R-Value Work:  0.120 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.121 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33DLC

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.61	α = 90
b = 63.5	β = 90
c = 75.44	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-26 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-08-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, 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: 2024-11-13
  Changes: Data collection, Structure summary