7CFY | pdb_00007cfy

Crystal Structure of YbeA CP74 W48F

PDB DOI: https://doi.org/10.2210/pdb7CFY/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-06-29 Released: 2021-06-30
Deposition Author(s): Liu, C.Y., Lai, C.H., Hsu, S.T.D., Lyu, P.C.
Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.307 (Depositor), 0.307 (DCC)
R-Value Work:
0.217 (Depositor), 0.218 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of YbeA CP74 W48F

Liu, C.Y., Lai, C.H., Hsu, S.T.D., Lyu, P.C.

To be published.

Macromolecule Content

Total Structure Weight: 70.41 kDa
Atom Count: 4,465
Modeled Residue Count: 587
Deposited Residue Count: 632
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal RNA large subunit methyltransferase H,Ribosomal RNA large subunit methyltransferase H	A, B, C, D	158	Escherichia coli K-12	Mutation(s): 1 Gene Names: rlmH, ybeA, b0636, JW0631 EC: 2.1.1.177
UniProt
Find proteins for P0A8I8 (Escherichia coli (strain K12)) Explore P0A8I8 Go to UniProtKB: P0A8I8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A8I8
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.307 (Depositor), 0.307 (DCC)
R-Value Work: 0.217 (Depositor), 0.218 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.137	α = 67.17
b = 57.833	β = 90.05
c = 69.629	γ = 90.15

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-06-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	--

Revision History (Full details and data files)

Version 1.0: 2021-06-30
Type: Initial release
Version 1.1: 2023-11-29
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.