3LYD | pdb_00003lyd

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 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

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 
• Modeled 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 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

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
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary