3SM3 | pdb_00003sm3

Crystal Structure of SAM-dependent methyltransferases Q8PUK2_METMA from Methanosarcina mazei. Northeast Structural Genomics Consortium Target MaR262.

PDB DOI: https://doi.org/10.2210/pdb3SM3/pdb

Classification: TRANSFERASE
Organism(s): Methanosarcina mazei Go1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2011-06-27 Released: 2011-07-20
Deposition Author(s): Vorobiev, S., Neely, H., Seetharaman, J., Snyder, A., Patel, P., Xiao, R., Ciccosanti, C., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.246 (Depositor), 0.252 (DCC)
R-Value Work:
0.192 (Depositor), 0.195 (DCC)
R-Value Observed:
0.195 (Depositor)

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

Literature

Crystal Structure of SAM-dependent methyltransferases Q8PUK2_METMA from Methanosarcina mazei.

Vorobiev, S., Neely, H., Seetharaman, J., Snyder, A., Patel, P., Xiao, R., Ciccosanti, C., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 27.16 kDa
Atom Count: 1,803
Modeled Residue Count: 212
Deposited Residue Count: 235
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAM-dependent methyltransferases	A	235	Methanosarcina mazei Go1	Mutation(s): 1 Gene Names: MM_2332
UniProt
Find proteins for Q8PUK2 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PUK2 Go to UniProtKB: Q8PUK2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8PUK2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.246 (Depositor), 0.252 (DCC)
R-Value Work: 0.192 (Depositor), 0.195 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.589	α = 90
b = 51.589	β = 90
c = 207.028	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-07-20

Deposition Author(s):

Seetharaman, J.

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2011-07-20
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations