3RHG | pdb_00003rhg

Crystal structure of amidohydrolase pmi1525 (target efi-500319) from proteus mirabilis hi4320

• PDB DOI: https://doi.org/10.2210/pdb3RHG/pdb

• Classification: HYDROLASE
• Organism(s): Proteus mirabilis HI4320
• Mutation(s): No 


• Deposited: 2011-04-11 Released: 2011-04-27 
• Deposition Author(s): Patskovsky, Y., Hillerich, B., Seidel, R.D., Zencheck, W.D., Toro, R., Imker, H.J., 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: 1.53 Å
• R-Value Free: 
  0.156 (Depositor), 0.162 (DCC) 
• R-Value Work: 
  0.120 (Depositor), 0.127 (DCC) 
• R-Value Observed: 
  0.121 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Amidohydrolase Pmi1525 from Proteus Mirabilis Hi4320

Patskovsky, Y., Hillerich, B., Seidel, R.D., Zencheck, W.D., Toro, R., Imker, H.J., Raushel, F.M., Gerlt, J.A., 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: 41.05 kDa 
• Atom Count: 3,456 
• Modeled Residue Count: 363 
• Deposited Residue Count: 365 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative phophotriesterase	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAC	E [auth A]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
BEZ	D [auth A]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNL	G [auth A], H [auth A], I [auth A]	Unknown ligand PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.156 (Depositor), 0.162 (DCC) 
• R-Value Work:  0.120 (Depositor), 0.127 (DCC) 
• R-Value Observed: 0.121 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.203	α = 90
b = 101.203	β = 90
c = 65.614	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-27 
Deposition Author(s): Patskovsky, Y., Hillerich, B., Seidel, R.D., Zencheck, W.D., Toro, R., Imker, H.J., Raushel, F.M., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2011-04-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description