4N7T

Crystal structure of phosphorylated phosphopentomutase from streptococcus mutans

• PDB DOI: https://doi.org/10.2210/pdb4N7T/pdb

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


• Deposited: 2013-10-16 Released: 2013-11-06 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Bonanno, J., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC), New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.203 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

Starting Model: experimental

Literature

Crystal structure of phosphorylated phosphopentomutase from streptococcus mutans

Fedorov, A.A., Fedorov, E.V., Bonanno, J., Burley, S.K., Almo, S.C.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 91.48 kDa 
• Atom Count: 6,596 
• Modelled Residue Count: 803 
• Deposited Residue Count: 826 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopentomutase	A, B	413	Streptococcus mutans UA159	Mutation(s): 0  Gene Names: deoB, SMU_1233 EC: 5.4.2.7
UniProt
Find proteins for Q8DTU0 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DTU0  Go to UniProtKB:  Q8DTU0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	I [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	E [auth A], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	C [auth A], D [auth A], K [auth B], L [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
AZI	H [auth A], N [auth B]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A, B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.203 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.788	α = 90
b = 63.687	β = 98.85
c = 104.765	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-06 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Bonanno, J., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC), New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-11-06
  Type: Initial release
  
• Version 1.1: 2013-11-27
  Changes: Structure summary
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Refinement description