3IEF | pdb_00003ief

Crystal structure of tRNA guanine-n1-methyltransferase from Bartonella henselae using MPCS.

PDB DOI: https://doi.org/10.2210/pdb3IEF/pdb

Classification: TRANSFERASE, RNA BINDING PROTEIN
Organism(s): Bartonella henselae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-07-22 Released: 2009-08-11
Deposition Author(s): Edwards, T.E., Stahl, G., Gerdts, C.J., Staker, B.L., Accelerated Technologies Center for Gene to 3D Structure (ATCG3D), Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.225 (Depositor), 0.202 (DCC)
R-Value Work:
0.195 (Depositor), 0.194 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of tRNA guanine-n1-methyltransferase from Bartonella henselae using MPCS.

Edwards, T.E., Stahl, G., Gerdts, C.J., Staker, B.L., Accelerated Technologies Center for Gene to 3D Structure (ATCG3D), Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 51.16 kDa
Atom Count: 3,380
Modeled Residue Count: 439
Deposited Residue Count: 466
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A, B	233	Bartonella henselae	Mutation(s): 0 Gene Names: trmD, BH15820 EC: 2.1.1.31 (PDB Primary Data), 2.1.1.228 (UniProt)
UniProt
Find proteins for Q6G1R9 (Bartonella henselae (strain ATCC 49882 / DSM 28221 / CCUG 30454 / Houston 1)) Explore Q6G1R9 Go to UniProtKB: Q6G1R9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6G1R9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.225 (Depositor), 0.202 (DCC)
R-Value Work: 0.195 (Depositor), 0.194 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.017	α = 90
b = 84.467	β = 90
c = 97.192	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-08-11

Deposition Author(s):

Accelerated Technologies Center for Gene to 3D Structure (ATCG3D)

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2009-08-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, 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.