2OBV

Crystal structure of the human S-adenosylmethionine synthetase 1 in complex with the product

• PDB DOI: https://doi.org/10.2210/pdb2OBV/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-12-20 Released: 2007-01-02 
• Deposition Author(s): Pilka, E.S., Shafqat, N., Kavanagh, K.L., Cooper, C., Hozjan, V., Turnbull, A., von Delft, F., Arrowsmith, C.H., Edwards, A., Weigelt, J., Sundstrom, M., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.183 
• R-Value Work: 0.139 
• R-Value Observed: 0.141 

Starting Models: experimental

Literature

Crystal structure of the human S-adenosylmethionine synthetase 1 in complex with the product.

Pilka, E.S., Shafqat, N., Kavanagh, K.L., Cooper, C., Hozjan, V., Turnbull, A., von Delft, F., Arrowsmith, C.H., Edwards, A., Weigelt, J., Sundstrom, M., Oppermann, U., Structural Genomics Consortium (SGC)

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: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 43.67 kDa 
• Atom Count: 3,350 
• Modelled Residue Count: 384 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine synthetase isoform type-1	A	384	Homo sapiens	Mutation(s): 0  Gene Names: MAT1A, AMS1, MATA1 EC: 2.5.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for Q00266 (Homo sapiens) Explore Q00266  Go to UniProtKB:  Q00266
PHAROS:  Q00266 GTEx:  ENSG00000151224

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	D [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
PG4	E [auth A], F [auth A], G [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
NA	B [auth A], C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.183 
• R-Value Work: 0.139 
• R-Value Observed: 0.141 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.404	α = 90
b = 95.016	β = 90
c = 115.773	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-02 
Deposition Author(s): Pilka, E.S., Shafqat, N., Kavanagh, K.L., Cooper, C., Hozjan, V., Turnbull, A., von Delft, F., Arrowsmith, C.H., Edwards, A., Weigelt, J., Sundstrom, M., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-01-02
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2018-01-31
  Changes: Database references, Structure summary
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description