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), 0.228 (DCC)
R-Value Work:
0.203 (Depositor), 0.198 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3KNU

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

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.228 (DCC)
R-Value Work: 0.203 (Depositor), 0.198 (DCC)
R-Value Observed: 0.205 (Depositor)

Diffraction Data:

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

View more in-depth experimental data

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 is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.