3EEI | pdb_00003eei

Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from neisseria meningitidis in complex with methylthio-immucillin-A

• PDB DOI: https://doi.org/10.2210/pdb3EEI/pdb

• Classification: HYDROLASE
• Organism(s): Neisseria meningitidis serogroup B
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-04 Released: 2009-09-08 
• Deposition Author(s): Ho, M., Rinaldo-matthis, A., Brown, R.L., Norris, G.E., Tyler, P.C., Furneaux, R.H., Almo, S.C., Schramm, V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.215 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.184 (Depositor) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from neisseria meningitidis in complex with methylthio-immucillin-A

Ho, M., Rinaldo-matthis, A., Brown, R.L., Norris, G.E., Tyler, P.C., Furneaux, R.H., Almo, S.C., Schramm, V.L.

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)

Macromolecule Content 

• Total Structure Weight: 50.04 kDa 
• Atom Count: 3,607 
• Modeled Residue Count: 462 
• Deposited Residue Count: 466 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-methylthioadenosine nucleosidase/S-adenosylhomocysteine nucleosidase	A, B	233	Neisseria meningitidis serogroup B	Mutation(s): 0  Gene Names: pfs EC: 3.2.2.16 (PDB Primary Data), 3.2.2.9 (PDB Primary Data)
UniProt
Find proteins for Q9K054 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q9K054  Go to UniProtKB:  Q9K054

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTM	C [auth A], D [auth B]	(3S,4R)-2-(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-5-[(METHYLSULFANYL)METHYL]PYRROLIDINE-3,4-DIOL C12 H19 N5 O2 S YLCQGEBEQIBOOJ-BOFBLULFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.215 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.184 (Depositor) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.359	α = 90
b = 40.897	β = 109.22
c = 83.612	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-08 
Deposition Author(s): Ho, M., Rinaldo-matthis, A., Brown, R.L., Norris, G.E., Tyler, P.C., Furneaux, R.H., Almo, S.C., Schramm, V.L.

Revision History  

• Version 1.0: 2009-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations