7CEM | pdb_00007cem

Crystal Structure of YbeA CP74 W7F

• PDB DOI: https://doi.org/10.2210/pdb7CEM/pdb

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


• Deposited: 2020-06-23 Released: 2021-06-23 
• Deposition Author(s): Liu, C.Y., Wu, C.Y., Lai, C.H., Hsu, S.T.D., Lyu, P.C.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 
  0.273 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of YbeA CP74 W7F

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.2 kDa 
• Atom Count: 2,453 
• Modeled Residue Count: 312 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal RNA large subunit methyltransferase H,Ribosomal RNA large subunit methyltransferase H	A, B	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free:  0.273 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.784	α = 90
b = 128.784	β = 90
c = 115.964	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-23 
Deposition Author(s): Liu, C.Y., Wu, C.Y., Lai, C.H., Hsu, S.T.D., Lyu, P.C.

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

Revision History  

• Version 1.0: 2021-06-23
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description