4YOK | pdb_00004yok

Crystal structure of a DUF3823 family protein (PARMER_04126) from Parabacteroides merdae ATCC 43184 at 1.80 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4YOK/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Parabacteroides merdae ATCC 43184
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-11 Released: 2015-03-25 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.214 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Crystal structure of a DUF3823 family protein (PARMER_04126) from Parabacteroides merdae ATCC 43184 at 1.80 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 22.69 kDa 
• Atom Count: 1,724 
• Modeled Residue Count: 199 
• Deposited Residue Count: 204 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative flagellar protein FliS	A	204	Parabacteroides merdae ATCC 43184	Mutation(s): 0  Gene Names: PARMER_04126

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.214 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m31c7p

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.866	α = 90
b = 66.212	β = 90
c = 68.593	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XDS	data scaling
XSCALE	data scaling
BUSTER-TNT	refinement
SHELXD	phasing
BUSTER	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-25 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2015-03-25
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary