3ISI | pdb_00003isi

Crystal structure of Sco3058 with bound inhibitor L-Ala-L-Asp Phosphinodipeptide

• PDB DOI: https://doi.org/10.2210/pdb3ISI/pdb

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


• Deposited: 2009-08-25 Released: 2010-08-04 
• Deposition Author(s): Nguyen, T.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.229 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Sco3058 with bound inhibitor L-Ala-L-Asp Phosphinodipeptide

Nguyen, T.T., Cummings, J.A., Tsai, C.-L., Barondeau, D.P., Raushel, F.M.

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: 43.68 kDa 
• Atom Count: 3,354 
• Modeled Residue Count: 392 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
renal dipeptidase	A [auth X]	400	Streptomyces coelicolor	Mutation(s): 0
UniProt
Find proteins for Q93J45 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q93J45  Go to UniProtKB:  Q93J45

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B88	B [auth X]	(2S)-2-{[(S)-[(1R)-1-aminoethyl](hydroxy)phosphoryl]methyl}butanedioic acid C7 H14 N O6 P LWODXTSWCZWQHR-RFZPGFLSSA-N
ZN	C [auth X], D [auth X]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.229 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.69	α = 90
b = 96.69	β = 90
c = 104.6	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASES	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-04 
Deposition Author(s): Nguyen, T.T.

Revision History  

• Version 1.0: 2010-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description