3KEV | pdb_00003kev

X-ray crystal structure of a DCUN1 domain-containing protein from Galdieria sulfuraria

• PDB DOI: https://doi.org/10.2210/pdb3KEV/pdb

• Classification: structural genomics, unknown function
• Organism(s): Galdieria sulphuraria
• Mutation(s): No 


• Deposited: 2009-10-26 Released: 2009-12-01 
• Deposition Author(s): Burgie, E.S., Bingman, C.A., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.178 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.155 (Depositor) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

Structural architecture of Galdieria sulphuraria DCN1L.

Burgie, E.S., Bingman, C.A., Makino, S., Wesenberg, G.E., Pan, X., Fox, B.G., Phillips, G.N.

(2011) Proteins 79: 1329-1336

• PubMed: 21387409 
• DOI: https://doi.org/10.1002/prot.22937
• Primary Citation Related Structures: 
  3KEV

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Organizational Affiliation: 
• Department of Genetics, Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, Madison Wisconsin 53706-1544, USA.

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: 23.54 kDa 
• Atom Count: 1,920 
• Modeled Residue Count: 184 
• Deposited Residue Count: 199 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galieria sulfuraria DCUN1 domain-containing protein	A	199	Galdieria sulphuraria	Mutation(s): 0
UniProt
Find proteins for D1MPT4 (Galdieria sulphuraria) Explore D1MPT4  Go to UniProtKB:  D1MPT4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	C [auth A], D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.178 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.155 (Depositor) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.743	α = 90
b = 52.422	β = 111.17
c = 49.113	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
SHARP	phasing
DM	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-01 
Deposition Author(s): Burgie, E.S., Bingman, C.A., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2009-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary