4FGM | pdb_00004fgm

Crystal structure of the aminopeptidase N family protein Q5QTY1 from Idiomarina loihiensis. Northeast Structural Genomics Consortium Target IlR60.

• PDB DOI: https://doi.org/10.2210/pdb4FGM/pdb

• Classification: HYDROLASE
• Organism(s): Idiomarina loihiensis L2TR
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-06-04 Released: 2012-08-01 
• Deposition Author(s): Vorobiev, S., Su, M., Tong, T., Kohan, E., Wang, D., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.209 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Crystal structure of the aminopeptidase N family protein Q5QTY1 from Idiomarina loihiensis.

Vorobiev, S., Su, M., Tong, T., Kohan, E., Wang, D., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 68.71 kDa 
• Atom Count: 4,940 
• Modeled Residue Count: 587 
• Deposited Residue Count: 597 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase N family protein	A	597	Idiomarina loihiensis L2TR	Mutation(s): 0  Gene Names: IL1258 EC: 3.4.11.2
UniProt
Find proteins for Q5QTY1 (Idiomarina loihiensis (strain ATCC BAA-735 / DSM 15497 / L2-TR)) Explore Q5QTY1  Go to UniProtKB:  Q5QTY1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAE	B [auth A]	MALEIC ACID C4 H4 O4 VZCYOOQTPOCHFL-UPHRSURJSA-N
ZN	C [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: 2.39 Å
• R-Value Free:  0.209 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.657	α = 90
b = 119.657	β = 90
c = 220.134	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXDE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-01 
Deposition Author(s): Vorobiev, S., Su, M., Tong, T., Kohan, E., Wang, D., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2012-08-01
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Author supporting evidence
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary