4QSF | pdb_00004qsf

CRYSTAL STRUCTURE of AMIDOHYDROLASE PMI1525 (TARGET EFI-500319) FROM PROTEUS MIRABILIS HI4320, A COMPLEX WITH BUTYRIC ACID AND MANGANESE

• PDB DOI: https://doi.org/10.2210/pdb4QSF/pdb

• Classification: HYDROLASE
• Organism(s): Proteus mirabilis HI4320
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-07-03 Released: 2014-07-30 
• Deposition Author(s): Patskovsky, Y., Toro, R., Xiang, D.F., Raushel, F.M., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.181 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Amidohydrolase Pmi1525 from Proteus Mirabilis Hi4320

Patskovsky, Y., Toro, R., Xiang, D.F., Raushel, F.M., Almo, S.C.

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: 40.95 kDa 
• Atom Count: 3,210 
• Modeled Residue Count: 354 
• Deposited Residue Count: 365 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidohydrolase Pmi1525	A	365	Proteus mirabilis HI4320	Mutation(s): 0  Gene Names: PMI1525
UniProt
Find proteins for B4EXV8 (Proteus mirabilis (strain HI4320)) Explore B4EXV8  Go to UniProtKB:  B4EXV8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BUA	D [auth A]	butanoic acid C4 H8 O2 FERIUCNNQQJTOY-UHFFFAOYSA-N
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.181 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.269	α = 90
b = 101.269	β = 90
c = 65.493	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-30 
Deposition Author(s): Patskovsky, Y., Toro, R., Xiang, D.F., Raushel, F.M., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2014-07-30
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary