3S2N

Crystal structure of dipeptidase from Streptomyces coelicolor complexed with phosphinate pseudodipeptide L-Tyr-D-Asp

• PDB DOI: https://doi.org/10.2210/pdb3S2N/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Streptomyces coelicolor
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-05-16 Released: 2011-06-22 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Cummings, J., Raushel, F.M., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.164 
• R-Value Work: 0.155 
• R-Value Observed: 0.155 

Literature

Crystal structure of dipeptidase from Streptomyces coelicolor complexed with phosphinate pseudodipeptide L-Tyr-D-Asp

Fedorov, A.A., Fedorov, E.V., Cummings, J., Raushel, F.M., 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)

Macromolecule Content

• Total Structure Weight: 44.2 kDa 
• Atom Count: 3,711 
• Modelled Residue Count: 393 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dipeptidase	A	400	Streptomyces coelicolor	Mutation(s): 0  Gene Names: SCO3058, SCBAC19G2.13c
UniProt
Find proteins for Q93J45 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q93J45  Go to UniProtKB:  Q93J45

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P4D	B [auth A]	(2R)-2-{[(S)-[(1R)-1-amino-2-(4-hydroxyphenyl)ethyl](hydroxy)phosphoryl]methyl}butanedioic acid C13 H18 N O7 P UESSIRUCJXFQBC-GXSJLCMTSA-N
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.164 
• R-Value Work: 0.155 
• R-Value Observed: 0.155 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.922	α = 90
b = 96.922	β = 90
c = 104.711	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-22 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Cummings, J., Raushel, F.M., Almo, S.C.

Revision History  

• Version 1.0: 2011-06-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description