4KDZ | pdb_00004kdz

Crystal structure of tRNA/rRNA methyltransferase YibK from Escherichia coli (Target NYSGRC-012599)

PDB DOI: https://doi.org/10.2210/pdb4KDZ/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli UTI89
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-04-25 Released: 2013-08-07
Deposition Author(s): Kim, J., Toro, R., Bhosle, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.227 (Depositor), 0.227 (DCC)
R-Value Work:
0.185 (Depositor), 0.185 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of tRNA/rRNA methyltransferase YibK from Escherichia coli (Target NYSGRC-012599)

Kim, J., Toro, R., Bhosle, R., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 17.75 kDa
Atom Count: 1,304
Modeled Residue Count: 156
Deposited Residue Count: 157
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (cytidine(34)-2'-O)-methyltransferase	A	157	Escherichia coli UTI89	Mutation(s): 0 Gene Names: b3606, JW3581, trmL, UTI89_C4147, yibK EC: 2.1.1.207
UniProt
Find proteins for Q1R4Y9 (Escherichia coli (strain UTI89 / UPEC)) Explore Q1R4Y9 Go to UniProtKB: Q1R4Y9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q1R4Y9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.227 (Depositor), 0.227 (DCC)
R-Value Work: 0.185 (Depositor), 0.185 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.435	α = 90
b = 84.435	β = 90
c = 78.654	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-08-07

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-08-07
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Refinement description

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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.