7WDQ | pdb_00007wdq

DsyB in complex with SAM

PDB DOI: https://doi.org/10.2210/pdb7WDQ/pdb

Classification: TRANSFERASE
Organism(s): Nisaea denitrificans DSM 18348
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-12-22 Released: 2022-06-01
Deposition Author(s): Li, C.Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.253 (Depositor), 0.250 (DCC)
R-Value Work:
0.192 (Depositor), 0.190 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Mechanistic insights into the key marine dimethylsulfoniopropionate synthesis enzyme DsyB/DSYB.

Li, C.Y., Crack, J.C., Newton-Payne, S., Murphy, A.R.J., Chen, X.L., Pinchbeck, B.J., Zhou, S., Williams, B.T., Peng, M., Zhang, X.H., Chen, Y.

(2022) mLife

DOI: https://doi.org/10.1002/mlf2.12030

Macromolecule Content

Total Structure Weight: 145.94 kDa
Atom Count: 10,316
Modeled Residue Count: 1,323
Deposited Residue Count: 1,348
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAM-dependent MTHB methyltransferase	A, B, C, D	337	Nisaea denitrificans DSM 18348	Mutation(s): 0
UniProt
Find proteins for A0A979HMS8 (Nisaea denitrificans DSM 18348) Explore A0A979HMS8 Go to UniProtKB: A0A979HMS8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A979HMS8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM (Subject of Investigation/LOI) Query on SAM Download Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.253 (Depositor), 0.250 (DCC)
R-Value Work: 0.192 (Depositor), 0.190 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.49	α = 90
b = 115.931	β = 90
c = 153.097	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-06-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-06-01
Type: Initial release
Version 1.1: 2022-08-03
Changes: Database references
Version 1.2: 2024-05-29
Changes: Data collection

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.