6GBN

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Cytophaga hutchinsonii in complex with adenosine

• PDB DOI: https://doi.org/10.2210/pdb6GBN/pdb

• Classification: HYDROLASE
• Organism(s): Cytophaga hutchinsonii ATCC 33406
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-04-15 Released: 2018-08-08 
• Deposition Author(s): Czyrko, J., Jaskolski, M., Brzezinski, K.
• Funding Organization(s): National Science Centre (Poland)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.231 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 

Starting Model: experimental

Literature

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Cytophaga hutchinsonii, a case of combination of crystallographic and non-crystallographic symmetry.

Czyrko, J., Jaskolski, M., Brzezinski, K.

(2018) Croat Chem Acta 91

• DOI: https://doi.org/10.5562/cca3345

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 196.33 kDa 
• Atom Count: 14,484 
• Modelled Residue Count: 1,732 
• Deposited Residue Count: 1,752 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B, C, D	438	Cytophaga hutchinsonii ATCC 33406	Mutation(s): 0  Gene Names: sahH, ahcY, CHU_0610 EC: 3.3.1.1

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	F [auth A], J [auth B], N [auth C], Q [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ADN	E [auth A], I [auth B], M [auth C], P [auth D]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N
PG4	H [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	L [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
NA	G [auth A], K [auth B], O [auth C], R [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.231 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18150/repod.4000773

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.275	α = 90
b = 102.445	β = 90
c = 188.919	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Czyrko, J., Jaskolski, M., Brzezinski, K.

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Funding Organization	Location	Grant Number
National Science Centre (Poland)	Poland	OPUS 2013/09/B/NZ1/01880

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description