3LKD | pdb_00003lkd

Crystal Structure of the type I restriction-modification system methyltransferase subunit from Streptococcus thermophilus, Northeast Structural Genomics Consortium Target SuR80

PDB DOI: https://doi.org/10.2210/pdb3LKD/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus thermophilus LMG 18311
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-01-27 Released: 2010-02-09
Deposition Author(s): Vorobiev, S., Su, M., Seetharaman, J., Mao, M., Xiao, R., Foote, E.L., Ciccosanti, C., Wang, D., 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: 2.25 Å
R-Value Free:
0.210 (Depositor), 0.205 (DCC)
R-Value Work:
0.186 (Depositor), 0.187 (DCC)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Northeast Structural Genomics Consortium Target SuR80

Vorobiev, S., Su, M., Seetharaman, J., Mao, M., Xiao, R., Foote, E.L., Ciccosanti, C., Wang, D., 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: 124.39 kDa
Atom Count: 7,930
Modeled Residue Count: 940
Deposited Residue Count: 1,084
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type I restriction-modification system methyltransferase subunit	A, B	542	Streptococcus thermophilus LMG 18311	Mutation(s): 0 Gene Names: hsdM1, stu0711 EC: 2.1.1.72
UniProt
Find proteins for Q5M500 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M500 Go to UniProtKB: Q5M500
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5M500
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 2.25 Å
R-Value Free: 0.210 (Depositor), 0.205 (DCC)
R-Value Work: 0.186 (Depositor), 0.187 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.866	α = 90
b = 83.128	β = 98.13
c = 96.678	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-02-09

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-02-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Structure summary