4M1A | pdb_00004m1a

Crystal structure of a Domain of unknown function (DUF1904) from Sebaldella termitidis ATCC 33386

• PDB DOI: https://doi.org/10.2210/pdb4M1A/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Sebaldella termitidis ATCC 33386
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-08-02 Released: 2013-08-14 
• Deposition Author(s): Kumaran, D., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Al Obaidi, N., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.206 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Crystal structure of a Domain of unknown function (DUF1904) from Sebaldellatermitidis ATCC 33386

Kumaran, D., Almo, S.C., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.21 kDa 
• Atom Count: 1,893 
• Modeled Residue Count: 216 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B	126	Sebaldella termitidis ATCC 33386	Mutation(s): 0  Gene Names: Sterm_0053
UniProt
Find proteins for D1AJN4 (Sebaldella termitidis (strain ATCC 33386 / NCTC 11300)) Explore D1AJN4  Go to UniProtKB:  D1AJN4

Small Molecules

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: 1.90 Å
• R-Value Free:  0.206 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.283	α = 90
b = 90.283	β = 90
c = 37.099	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHELXE	model building
ARP/wARP	model building
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-14 
Deposition Author(s): Kumaran, D., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Al Obaidi, N., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-08-14
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary