3LYD

Crystal structure of Putative uncharacterized protein from Jonesia denitrificans

• PDB DOI: https://doi.org/10.2210/pdb3LYD/pdb

• Classification: Structural Genomics, Unknown function
• Organism(s): Jonesia denitrificans DSM 20603
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-02-26 Released: 2010-03-09 
• Deposition Author(s): Chang, C., Volkart, L., Bearden, J., Wu, D., Eisen, J., Kerfeld, C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.192 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

Crystal structure of Putative uncharacterized protein from Jonesia denitrificans

Chang, C., Volkart, L., Bearden, J., Wu, D., Eisen, J., Kerfeld, C., Joachimiak, A.

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: 36.28 kDa 
• Atom Count: 3,185 
• Modelled Residue Count: 318 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	161	Jonesia denitrificans DSM 20603	Mutation(s): 0  Gene Names: Jden_0139
UniProt
Find proteins for C7QYG7 (Jonesia denitrificans (strain ATCC 14870 / DSM 20603 / BCRC 15368 / CIP 55.134 / JCM 11481 / NBRC 15587 / NCTC 10816 / Prevot 55134)) Explore C7QYG7  Go to UniProtKB:  C7QYG7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.192 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.551	α = 90
b = 70.879	β = 90
c = 99.48	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Chang, C., Volkart, L., Bearden, J., Wu, D., Eisen, J., Kerfeld, C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description