3KNU | pdb_00003knu

Crystal structure of tRNA (guanine-N1)-methyltransferase from Anaplasma phagocytophilum

PDB DOI: https://doi.org/10.2210/pdb3KNU/pdb

Classification: TRANSFERASE
Organism(s): Anaplasma phagocytophilum str. HZ
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-11-12 Released: 2009-11-24
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.234 (Depositor), 0.230 (DCC)
R-Value Work:
0.203 (Depositor), 0.200 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of tRNA (guanine-N1)-methyltransferase from Anaplasma phagocytophilum

Edwards, T.E., Abendroth, J., Stahl, G., Sankaran, B., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 112.3 kDa
Atom Count: 6,379
Modeled Residue Count: 785
Deposited Residue Count: 1,012
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A, B, C, D	253	Anaplasma phagocytophilum str. HZ	Mutation(s): 0 Gene Names: trmD, APH_1267 EC: 2.1.1.31 (PDB Primary Data), 2.1.1.228 (UniProt)
UniProt
Find proteins for Q2GIL5 (Anaplasma phagocytophilum (strain HZ)) Explore Q2GIL5 Go to UniProtKB: Q2GIL5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2GIL5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.234 (Depositor), 0.230 (DCC)
R-Value Work: 0.203 (Depositor), 0.200 (DCC)
R-Value Observed: 0.205 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33KNU

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.291	α = 90
b = 104.304	β = 90
c = 99.105	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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-11-24

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2009-11-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Source and taxonomy, 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

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.