8SH4 | pdb_00008sh4

Crystal structure of the tRNA (m1G37) methyltransferase apoenzyme from Anaplasma phagocytophilum

PDB DOI: https://doi.org/10.2210/pdb8SH4/pdb
Entry: 8SH4 supersedes: 6UEV

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

Deposited: 2023-04-13 Released: 2024-04-17
Deposition Author(s): Jannotta, C., Edele, D., Levanti, D., Carson, M., Prucha, G., Caesar, J., Picchiello, C., Collins, K., Garland, E., Handley-Pendleton, J., Hernandez, V., Leffler, S., Williams, D., Stojanoff, V., Perez, A., Halloran, J., Bolen, R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.255 (Depositor), 0.279 (DCC)
R-Value Work:
0.202 (Depositor)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the m1G37 tRNA methyltransferase apoenzyme from Anaplasma phagocytophilum

Jannotta, C., Edele, D., Levanti, D., Carson, M., Prucha, G., Caesar, J., Collins, K., Garland, E., Handley-Pendleton, J., Hernandez, V., Leffler, S., Williams, D., Stojanoff, V., Perez, A., Halloran, J., Bolen, R.

To be published.

Macromolecule Content

Total Structure Weight: 24.16 kDa
Atom Count: 1,663
Modeled Residue Count: 218
Deposited Residue Count: 218
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A	218	Anaplasma phagocytophilum	Mutation(s): 0 Gene Names: trmD EC: 2.1.1.228
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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.255 (Depositor), 0.279 (DCC)
R-Value Work: 0.202 (Depositor)
R-Value Observed: 0.204 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.73	α = 90
b = 104.73	β = 90
c = 91.23	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-17

Deposition Author(s):

Handley-Pendleton, J.

This entry supersedes: 6UEV

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41GM111244
Department of Energy (DOE, United States)	United States	DE-SC0012704
Department of Energy (DOE, United States)	United States	KP1605010