3T0I | pdb_00003t0i

Crystal structure of complex of BT_2972 and AdoHcy, a methyltransferase from Bacteroides thetaiotaomicron

PDB DOI: https://doi.org/10.2210/pdb3T0I/pdb

Classification: TRANSFERASE
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-07-20 Released: 2011-09-07
Deposition Author(s): Kumar, V., Sivaraman, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.230 (Depositor), 0.245 (DCC)
R-Value Work:
0.210 (Depositor), 0.227 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of complex of BT_2972 and AdoHcy,a methyltransferase from Bacteroides thetaiotaomicron

Kumar, V., Sivaraman, J.

To be published.

Macromolecule Content

Total Structure Weight: 61.4 kDa
Atom Count: 4,175
Modeled Residue Count: 490
Deposited Residue Count: 526
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative methyltransferase	A, B	263	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: NP_811884.1
UniProt
Find proteins for Q8A3I2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A3I2 Go to UniProtKB: Q8A3I2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8A3I2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.230 (Depositor), 0.245 (DCC)
R-Value Work: 0.210 (Depositor), 0.227 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.642	α = 90
b = 74.525	β = 90
c = 117.221	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-09-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-09-07
Type: Initial release
Version 1.1: 2011-09-28
Changes: Refinement description
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.