3GU3

Crystal Structure of the methyltransferase BC_2162 in complex with S-Adenosyl-L-Homocysteine from Bacillus cereus, Northeast Structural Genomics Consortium Target BcR20

PDB DOI: https://doi.org/10.2210/pdb3GU3/pdb

Classification: TRANSFERASE
Organism(s): Bacillus cereus ATCC 14579
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-03-28 Released: 2009-04-07
Deposition Author(s): Forouhar, F., Neely, H., Seetharaman, J., Ciano, C., Ma, L., Zhao, L., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.212 (Depositor), 0.217 (DCC)
R-Value Work:
0.184 (Depositor), 0.189 (DCC)
R-Value Observed:
0.185 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Northeast Structural Genomics Consortium Target BcR20

Forouhar, F., Neely, H., Seetharaman, J., Ciano, C., Ma, L., Zhao, L., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 66.76 kDa
Atom Count: 4,777
Modelled Residue Count: 552
Deposited Residue Count: 568
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase	A, B	284	Bacillus cereus ATCC 14579	Mutation(s): 0 Gene Names: BC_2162 EC: 2.1.1
UniProt
Find proteins for Q81E32 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q81E32 Go to UniProtKB: Q81E32
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q81E32
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 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] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.212 (Depositor), 0.217 (DCC)
R-Value Work: 0.184 (Depositor), 0.189 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.793	α = 90
b = 90.793	β = 90
c = 122.627	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SnB	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-04-07

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-04-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2011-08-24
Changes: Structure summary
Version 1.3: 2017-11-01
Changes: Refinement description
Version 1.4: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.5: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary