3N58 | pdb_00003n58

Crystal structure of S-ADENOSYL-L-HOMOCYSTEINE hydrolase from brucella melitensis in ternary complex with NAD and adenosine, orthorhombic form

• PDB DOI: https://doi.org/10.2210/pdb3N58/pdb

• Classification: HYDROLASE
• Organism(s): Brucella abortus 2308
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-05-24 Released: 2010-06-02 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.235 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of S-adenosyl-L-homocysteine hydrolase from brucella melitensis in ternary complex with NAD and adenosine, orthorhombic form

SSGCID, Gardberg, A., Sankaran, B., Abendroth, J., Staker, B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 205.56 kDa 
• Atom Count: 14,819 
• Modeled Residue Count: 1,843 
• Deposited Residue Count: 1,856 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B, C, D	464	Brucella abortus 2308	Mutation(s): 0  Gene Names: ahcY, BAB1_2099 EC: 3.3.1.1 (PDB Primary Data), 3.13.2.1 (UniProt)
UniProt
Find proteins for Q2YQX8 (Brucella abortus (strain 2308)) Explore Q2YQX8  Go to UniProtKB:  Q2YQX8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	G [auth A], H [auth B], K [auth C], N [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ADN	F [auth A], J [auth C], M [auth D]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N
K	E [auth A], I [auth C], L [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.235 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33N58

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.45	α = 90
b = 165.23	β = 90
c = 184.14	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-02 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2010-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2012-03-21
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description