6GBN | pdb_00006gbn

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free:
0.231 (Depositor), 0.231 (DCC)
R-Value Work:
0.210 (Depositor), 0.216 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain N [auth C] SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B], N [auth C], Q [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D]
ADN Query on ADN Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], M [auth C], P [auth D]	ADENOSINE C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain P [auth D]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D]	G [auth A], K [auth B], O [auth C], R [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.231 (Depositor), 0.231 (DCC)
R-Value Work: 0.210 (Depositor), 0.216 (DCC)
R-Value Observed: 0.211 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-08-08

Deposition Author(s):

Czyrko, J.

Jaskolski, M.

Brzezinski, K.

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

Revision History (Full details and data files)

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