3M7V | pdb_00003m7v

Crystal structure of phosphopentomutase from streptococcus mutans

• PDB DOI: https://doi.org/10.2210/pdb3M7V/pdb
• Entry: 3M7V supersedes: 2I09

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


• Deposited: 2010-03-17 Released: 2010-04-07 
• Deposition Author(s): Fedorov, A.A., Bonanno, J., Fedorov, E.V., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.211 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Crystal structure of phosphopentomutase from streptococcus mutans

Fedorov, A.A., Bonanno, J., Fedorov, E.V., 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: 90.75 kDa 
• Atom Count: 6,466 
• Modeled Residue Count: 802 
• 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	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	C [auth A], D [auth A], F [auth B], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.211 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

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
SOLVE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-07 
Deposition Author(s): Fedorov, A.A., Bonanno, J., Fedorov, E.V., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)
• This entry supersedes: 2I09

Revision History  

• Version 1.0: 2010-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references