4H3Z

Crystal structure of a symmetric dimer of a tRNA (guanine-(N(1)-)-methyltransferase from Burkholderia phymatum bound to S-adenosyl homocystein in both half-sites

PDB DOI: https://doi.org/10.2210/pdb4H3Z/pdb

Classification: TRANSFERASE
Organism(s): Paraburkholderia phymatum STM815
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-09-14 Released: 2012-10-03
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.228
R-Value Work: 0.186
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Combining functional and structural genomics to sample the essential Burkholderia structome.

Baugh, L., Gallagher, L.A., Patrapuvich, R., Clifton, M.C., Gardberg, A.S., Edwards, T.E., Armour, B., Begley, D.W., Dieterich, S.H., Dranow, D.M., Abendroth, J., Fairman, J.W., Fox, D., Staker, B.L., Phan, I., Gillespie, A., Choi, R., Nakazawa-Hewitt, S., Nguyen, M.T., Napuli, A., Barrett, L., Buchko, G.W., Stacy, R., Myler, P.J., Stewart, L.J., Manoil, C., Van Voorhis, W.C.

(2013) PLoS One 8: e53851-e53851

PubMed: 23382856 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0053851
Primary Citation of Related Structures:
3D63, 3DAH, 3EIZ, 3EJ2, 3EK2, 3EZO, 3F0F, 3FTP, 3GK0, 3GK3, 3GVF, 3GWA, 3GWE, 3IML, 3SZ8, 3T4C, 3TML, 3TMQ, 3TXY, 3U7J, 3UE9, 3UK1, 3UK2, 3UND, 3UPT, 3URR, 3UW1, 3UW2, 3UW3, 3V2I, 3V7N, 3V8H, 3V9O, 3V9P, 3VAV, 4DDO, 4DFE, 4DHE, 4DHK, 4DUT, 4DZ4, 4E4T, 4EFI, 4EG0, 4EGJ, 4EK2, 4EQY, 4EWG, 4EXQ, 4F2G

PubMed Abstract:
The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite.

Organizational Affiliation

Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America.

Macromolecule Content

Total Structure Weight: 62.42 kDa
Atom Count: 4,163
Modelled Residue Count: 505
Deposited Residue Count: 552
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A, B	276	Paraburkholderia phymatum STM815	Mutation(s): 0 Gene Names: Bphy_0771, trmD EC: 2.1.1.228
UniProt
Find proteins for B2JF31 (Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815)) Explore B2JF31 Go to UniProtKB: B2JF31
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2JF31
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.228
R-Value Work: 0.186
R-Value Observed: 0.189
Space Group: C 2 2 2₁
Diffraction Data: https://doi.org/10.18430/M34H3Z

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.85	α = 90
b = 188.09	β = 90
c = 127.68	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-10-03

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2012-10-03
Type: Initial release
Version 1.1: 2013-10-30
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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4H3Z

Crystal structure of a symmetric dimer of a tRNA (guanine-(N(1)-)-methyltransferase from Burkholderia phymatum bound to S-adenosyl homocystein in both half-sites

Combining functional and structural genomics to sample the essential Burkholderia structome.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)