3DXX | pdb_00003dxx

Crystal structure of EcTrmB

PDB DOI: https://doi.org/10.2210/pdb3DXX/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-25 Released: 2009-05-19
Deposition Author(s): Zhou, H.H., Liu, Q., Gao, Y.X., Teng, M.K., Niu, L.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.227 (Depositor), 0.231 (DCC)
R-Value Work:
0.193 (Depositor), 0.194 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3DXX

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

Literature

Monomeric tRNA (m(7)G46) methyltransferase from Escherichia coli presents a novel structure at the function-essential insertion

Zhou, H., Liu, Q., Yang, W., Gao, Y., Teng, M., Niu, L.

(2009) Proteins 76: 512-515

PubMed: 19373903 Search on PubMed
DOI: https://doi.org/10.1002/prot.22413
Primary Citation Related Structures:
3DXX, 3DXY, 3DXZ

Organizational Affiliation

University of Science & Technology of China, Hefei, Anhui, China.

Macromolecule Content

Total Structure Weight: 24.92 kDa
Atom Count: 1,836
Modeled Residue Count: 208
Deposited Residue Count: 218
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(7)-)-methyltransferase	A	218	Escherichia coli K-12	Mutation(s): 0 Gene Names: trmB EC: 2.1.1.33
UniProt
Find proteins for P0A8I5 (Escherichia coli (strain K12)) Explore P0A8I5 Go to UniProtKB: P0A8I5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A8I5
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: 2.05 Å
R-Value Free: 0.227 (Depositor), 0.231 (DCC)
R-Value Work: 0.193 (Depositor), 0.194 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.42	α = 90
b = 47.01	β = 90.01
c = 58.64	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-05-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-05-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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