7Y8O | pdb_00007y8o

Structure of ScIRED-R3-V4 from Streptomyces clavuligerus in complex with 5-(3-fluorophenyl)-3,4-dihydro-2H-pyrrole

• PDB DOI: https://doi.org/10.2210/pdb7Y8O/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Streptomyces clavuligerus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2022-06-24 Released: 2023-03-22 
• Deposition Author(s): Zhang, L.L., Liu, W.D., Shi, M., Huang, J.W., Yang, Y., Chen, C.C., Guo, R.T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Structure of ScIRED-R3-V4 from Streptomyces clavuligerus in complex with 5-(3-fluorophenyl)-3,4-dihydro-2H-pyrrole

Zhang, L.L., Liu, W.D., Shi, M., Huang, J.W., Yang, Y., Chen, C.C., Guo, R.T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.5 kDa 
• Atom Count: 4,681 
• Modeled Residue Count: 573 
• Deposited Residue Count: 580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SciR	A, B	290	Streptomyces clavuligerus	Mutation(s): 0
UniProt
Find proteins for E2PUR9 (Streptomyces clavuligerus) Explore E2PUR9  Go to UniProtKB:  E2PUR9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	C [auth A], E [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
Q0R (Subject of Investigation/LOI)	D [auth B]	2-[2,5-bis(fluoranyl)phenyl]pyrrolidine C10 H11 F2 N NCXSNNVYILYEBC-SNVBAGLBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.797	α = 90
b = 81.358	β = 90
c = 93.127	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
SAINT	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-22 
Deposition Author(s): Zhang, L.L., Liu, W.D., Shi, M., Huang, J.W., Yang, Y., Chen, C.C., Guo, R.T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-03-22
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection
• Version 1.2: 2023-11-29
  Changes: Refinement description
• Version 1.3: 2024-04-03
  Changes: Database references