4G89 | pdb_00004g89

Crystal structure of k. pneumoniae mta/adohcy nucleosidase in complex with fragmented s-adenosyl-l-homocysteine

• PDB DOI: https://doi.org/10.2210/pdb4G89/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-07-23 Released: 2012-09-19 
• Deposition Author(s): Norris, G.E., Brown, R.L., Anderson, B.F., Tyler, P.C., Evans, G.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.220 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.160 (Depositor) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of k. pneumoniae mta/adohcy nucleosidase in complex with fragmented s-adenosyl-l-homocysteine

Norris, G.E., Brown, R.L., Anderson, B.F., Tyler, P.C., Evans, G.B.

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: 50.65 kDa 
• Atom Count: 3,822 
• Modeled Residue Count: 466 
• Deposited Residue Count: 474 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase	A, B	237	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0  Gene Names: KPN 00174, KPN78578_01730, KPN_00174, mtnN EC: 3.2.2.9
UniProt
Find proteins for A6T4W3 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6T4W3  Go to UniProtKB:  A6T4W3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	D [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ADE	C [auth A]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.220 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.160 (Depositor) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.346	α = 90
b = 59.242	β = 128.46
c = 82.926	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-19 
Deposition Author(s): Norris, G.E., Brown, R.L., Anderson, B.F., Tyler, P.C., Evans, G.B.

Revision History  

• Version 1.0: 2012-09-19
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-04-03
  Changes: Refinement description