5HX0 | pdb_00005hx0

Crystal structure of unknown function protein Dfer_1899 fromDyadobacter fermentans DSM 18053

• PDB DOI: https://doi.org/10.2210/pdb5HX0/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Dyadobacter fermentans DSM 18053
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-01-29 Released: 2016-02-17 
• Deposition Author(s): Chang, C., Duke, N., Clancy, S., Chhor, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• 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: 1.85 Å
• R-Value Free: 
  0.194 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

Crystal structure of unknown function protein Dfer_1899 fromDyadobacter fermentans DSM 18053

Chang, C., Duke, N., Clancy, S., Chhor, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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: 90.55 kDa 
• Atom Count: 6,583 
• Modeled Residue Count: 729 
• Deposited Residue Count: 804 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein Dfer_1899	A, B	402	Dyadobacter fermentans DSM 18053	Mutation(s): 0  Gene Names: Dfer_1899
UniProt
Find proteins for C6VW01 (Dyadobacter fermentans (strain ATCC 700827 / DSM 18053 / CIP 107007 / KCTC 52180 / NS114)) Explore C6VW01  Go to UniProtKB:  C6VW01

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	C [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	I [auth A], L [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	F [auth A], G [auth A], H [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	D [auth A], E [auth A], K [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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: 1.85 Å
• R-Value Free:  0.194 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.698	α = 90
b = 85.441	β = 90
c = 158.812	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing
SBC-Collect	data collection
ARP	model building
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-02-17 
Deposition Author(s): Chang, C., Duke, N., Clancy, S., Chhor, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115586

Revision History  

• Version 1.0: 2016-02-17
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Structure summary