4X3Q | pdb_00004x3q

Crystal structure of S-adenosylmethionine-dependent methyltransferase SibL in complex with SAH

• PDB DOI: https://doi.org/10.2210/pdb4X3Q/pdb

• Classification: LIGASE
• Organism(s): Streptosporangium sibiricum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-12-01 Released: 2015-11-25 
• Deposition Author(s): liu, J.S., Chen, S.C., Yang, C.S., Huang, C.H., Chen, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.248 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Crystal structure of S-adenosylmethionine-dependent methyltransferase SibL in complex with SAH

liu, J.S., Chen, S.C., Yang, C.S., Huang, C.H., Chen, Y.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 157.61 kDa 
• Atom Count: 10,783 
• Modeled Residue Count: 1,364 
• Deposited Residue Count: 1,420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SibL	A, B, C, D	355	Streptosporangium sibiricum	Mutation(s): 0  Gene Names: sibL
UniProt
Find proteins for C0LTM6 (Streptosporangium sibiricum) Explore C0LTM6  Go to UniProtKB:  C0LTM6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	E [auth A], F [auth B], G [auth C], H [auth D]	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, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.248 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.787	α = 90
b = 112.113	β = 90
c = 143.708	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-25 
Deposition Author(s): liu, J.S., Chen, S.C., Yang, C.S., Huang, C.H., Chen, Y.

Revision History  

• Version 1.0: 2015-11-25
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary