3L87 | pdb_00003l87

The Crystal Structure of smu.143c from Streptococcus mutans UA159

• PDB DOI: https://doi.org/10.2210/pdb3L87/pdb

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


• Deposited: 2009-12-30 Released: 2011-01-05 
• Deposition Author(s): Su, X.-D., Cao, Q., Liu, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.285 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

The Crystal Structure of smu.143c from Streptococcus mutans UA159

Su, X.-D., Cao, Q., Liu, X.

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: 26.59 kDa 
• Atom Count: 1,661 
• Modeled Residue Count: 200 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A	238	Streptococcus mutans UA159	Mutation(s): 0  Gene Names: smu.143c EC: 3.5.1.88
UniProt
Find proteins for Q8DWC2 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DWC2  Go to UniProtKB:  Q8DWC2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.285 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.589	α = 90
b = 55.621	β = 90
c = 85.778	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
MOLREP	phasing
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-05 
Deposition Author(s): Su, X.-D., Cao, Q., Liu, X.

Revision History  

• Version 1.0: 2011-01-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-11-12
  Changes: Other
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary