3GO9 | pdb_00003go9

Predicted insulinase family protease from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb3GO9/pdb

• Classification: HYDROLASE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-18 Released: 2009-04-07 
• Deposition Author(s): Osipiuk, J., Maltseva, N., Onopriyenko, O., Peterson, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.203 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

X-ray crystal structure of predicted insulinase family protease from Yersinia pestis.

Osipiuk, J., Maltseva, N., Onopriyenko, O., Peterson, S., Anderson, W.F., Joachimiak, A.

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: 55.74 kDa 
• Atom Count: 4,231 
• Modeled Residue Count: 458 
• Deposited Residue Count: 492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
insulinase family protease	A	492	Yersinia pestis	Mutation(s): 0  Gene Names: pqqL, y3837, YPO3991, YP_3354
UniProt
Find proteins for Q0WA27 (Yersinia pestis) Explore Q0WA27  Go to UniProtKB:  Q0WA27

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.203 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33go9

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.89	α = 90
b = 80.23	β = 99.34
c = 66.62	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-07 
Deposition Author(s): Osipiuk, J., Maltseva, N., Onopriyenko, O., Peterson, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary