5BP9

Crystal structure of SAM-dependent methyltransferase from Bacteroides fragilis in complex with S-Adenosyl-L-homocysteine

PDB DOI: https://doi.org/10.2210/pdb5BP9/pdb

Classification: TRANSFERASE
Organism(s): Bacteroides fragilis NCTC 9343
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-05-27 Released: 2015-06-10
Deposition Author(s): Gasiorowska, O.A., Shabalin, I.G., Handing, K.B., Cymborowski, M.T., Mason, D.V., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
Funding Organization(s): National Institutes of Health

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.179
R-Value Work: 0.132
R-Value Observed: 0.134

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of SAM-dependent methyltransferase fromBacteroides fragilis in complex with S-Adenosyl-L-homocysteine

Gasiorowska, O.A., Shabalin, I.G., Handing, K.B., Cymborowski, M.T., Mason, D., Bonanno, J., Seidel, R., Almo, S.C., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 33.09 kDa
Atom Count: 2,320
Modelled Residue Count: 237
Deposited Residue Count: 281
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative methyltransferase protein	A	281	Bacteroides fragilis NCTC 9343	Mutation(s): 0 Gene Names: BF9343_1312
UniProt
Find proteins for Q5LFK0 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / NCTC 9343 / Onslow)) Explore Q5LFK0 Go to UniProtKB: Q5LFK0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5LFK0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ETE Query on ETE Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₉ H₂₀ O₅ ZNYRFEPBTVGZDN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.179
R-Value Work: 0.132
R-Value Observed: 0.134
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M39013

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.732	α = 90
b = 70.66	β = 90
c = 78.743	γ = 90

Software Package:

Software Name	Purpose
BLU-MAX	data collection
HKL-3000	data reduction
HKL-3000	phasing
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-06-10

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Funding Organization	Location	Grant Number
National Institutes of Health	United States	--

Revision History (Full details and data files)

Version 1.0: 2015-06-10
Type: Initial release
Version 1.1: 2017-10-11
Changes: Advisory, Derived calculations, Refinement description, Source and taxonomy
Version 1.2: 2022-04-13
Changes: Database references, Structure summary

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5BP9

Crystal structure of SAM-dependent methyltransferase from Bacteroides fragilis in complex with S-Adenosyl-L-homocysteine

Crystal structure of SAM-dependent methyltransferase fromBacteroides fragilis in complex with S-Adenosyl-L-homocysteine

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)