5DUD | pdb_00005dud

Crystal structure of E. coli YbgJK

• PDB DOI: https://doi.org/10.2210/pdb5DUD/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-09-18 Released: 2016-09-28 
• Deposition Author(s): Arbing, M.A., Kaufmann, M., Shin, A., Medrano-Soto, A., Cascio, D., Eisenberg, D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.288 (Depositor), 0.314 (DCC) 
• R-Value Work: 
  0.268 (Depositor), 0.296 (DCC) 
• R-Value Observed: 
  0.269 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of E. coli YbgJK

Arbing, M.A., Kaufmann, M., Shin, A., Medrano-Soto, A., Cascio, D., Eisenberg, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 116.8 kDa 
• Atom Count: 7,451 
• Modeled Residue Count: 992 
• Deposited Residue Count: 1,056 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YbgK	A, C	310	Escherichia coli K-12	Mutation(s): 0  Gene Names: ybgK, b0712, JW0702 EC: 3.5.2.9
UniProt
Find proteins for P75745 (Escherichia coli (strain K12)) Explore P75745  Go to UniProtKB:  P75745

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
YbgJ	B, D	218	Escherichia coli K-12	Mutation(s): 0  Gene Names: ybgJ, b0711, JW0701 EC: 3.5.2.9
UniProt
Find proteins for P0AAV4 (Escherichia coli (strain K12)) Explore P0AAV4  Go to UniProtKB:  P0AAV4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.288 (Depositor), 0.314 (DCC) 
• R-Value Work:  0.268 (Depositor), 0.296 (DCC) 
• R-Value Observed: 0.269 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.11	α = 90
b = 88.78	β = 101.91
c = 83.7	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
MR-Rosetta	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-09-28 
Deposition Author(s): Arbing, M.A., Kaufmann, M., Shin, A., Medrano-Soto, A., Cascio, D., Eisenberg, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM071909-01A2

Revision History  

• Version 1.0: 2016-09-28
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2017-10-11
  Changes: Data collection
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description