2QNE

Crystal structure of putative methyltransferase (ZP_00558420.1) from Desulfitobacterium hafniense Y51 at 2.30 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2QNE/pdb

• Classification: TRANSFERASE
• Organism(s): Desulfitobacterium hafniense Y51
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-07-18 Released: 2007-08-14 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.204 
• R-Value Work: 0.158 
• R-Value Observed: 0.161 

Literature

Crystal structure of putative methyltransferase (ZP_00558420.1) from Desulfitobacterium hafniense Y51 at 2.30 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

Macromolecule Content

• Total Structure Weight: 111.76 kDa 
• Atom Count: 7,406 
• Modelled Residue Count: 951 
• Deposited Residue Count: 990 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative methyltransferase	A, B	495	Desulfitobacterium hafniense Y51	Mutation(s): 0  Gene Names: ZP_00558420.1, DSY3156 EC: 2.1.1.376
UniProt
Find proteins for Q24SP7 (Desulfitobacterium hafniense (strain Y51)) Explore Q24SP7  Go to UniProtKB:  Q24SP7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 2.30 Å
• R-Value Free: 0.204 
• R-Value Work: 0.158 
• R-Value Observed: 0.161 
• Space Group: P 3₂ 2 1
• Diffraction Data: https://doi.org/10.18430/M32QNE

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.863	α = 90
b = 123.863	β = 90
c = 122.844	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-14 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-08-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary