3L7V | pdb_00003l7v

Crystal structure of a hypothetical protein smu.1377c from Streptococcus mutans UA159

• PDB DOI: https://doi.org/10.2210/pdb3L7V/pdb

• Classification: TRANSCRIPTION
• Organism(s): Streptococcus mutans UA159
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-12-29 Released: 2010-07-21 
• Deposition Author(s): Su, X.-D., Fu, T.-M., Liu, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.259 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

The structure of the hypothetical protein smu.1377c from Streptococcus mutans suggests a role in tRNA modification

Fu, T.-M., Liu, X., Li, L., Su, X.-D.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 771-775

• PubMed: 20606270 
• DOI: https://doi.org/10.1107/S1744309110018944
• Primary Citation Related Structures: 
  3L7V


• PubMed Abstract: 
  

  Members of the Sua5_YciO_YrdC protein family are found in both eukaryotes and prokaryotes and possess a conserved alpha/beta twisted open-sheet fold. The Escherichia coli protein YrdC has been shown to be involved in modification of tRNA. The crystal structure of smu.1377c, a hypothetical protein from Streptococcus mutans, has been determined to 2.25 A resolution. From structure analysis and comparison, it is shown that smu.1377c is a member of the Sua5_YciO_YrdC family and that it may play the same role as E. coli YrdC.

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Organizational Affiliation: 
• The National Laboratory of Protein Engineering and Plant Genetic Engineering, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.41 kDa 
• Atom Count: 2,127 
• Modeled Residue Count: 256 
• Deposited Residue Count: 295 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein smu.1377c	A	295	Streptococcus mutans UA159	Mutation(s): 0  Gene Names: smu.1377c
UniProt
Find proteins for Q8DTG7 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DTG7  Go to UniProtKB:  Q8DTG7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 2.26 Å
• R-Value Free:  0.259 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.9	α = 90
b = 92.6	β = 90
c = 40.6	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
SHELXS	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-21 
Deposition Author(s): Su, X.-D., Fu, T.-M., Liu, X.

Revision History  

• Version 1.0: 2010-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-05-30
  Changes: Data collection
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary