9GVD | pdb_00009gvd

Structure of phosphonate monoester hydrolase from Rhizobium leguminosarum with vanadate

• PDB DOI: https://doi.org/10.2210/pdb9GVD/pdb

• Classification: HYDROLASE
• Organism(s): Rhizobium johnstonii 3841
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2024-09-24 Released: 2025-10-08 
• Deposition Author(s): Jonas, S., Hyvonen, M., Hollfelder, F.
• Funding Organization(s): European Union (EU), Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.162 (Depositor), 0.162 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.135 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Starting Model: experimental

Literature

Efficient leaving group stabilization and hydrophobic binding make Phosphonate Monoester Hydrolase (PMH) an exceptionally promiscuous enzyme

Mohamed, M.F., Jonas, S., Miton, C., van Loo, B., Hyvonen, M., Hollfelder, F.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 61.34 kDa 
• Atom Count: 4,852 
• Modeled Residue Count: 512 
• Deposited Residue Count: 543 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multifunctional alkaline phosphatase superfamily protein pRL90232	A	543	Rhizobium johnstonii 3841	Mutation(s): 0  Gene Names: pRL90232 EC: 3.1.4 (PDB Primary Data), 3.1.3 (PDB Primary Data)
UniProt
Find proteins for Q1M964 (Rhizobium johnstonii (strain DSM 114642 / LMG 32736 / 3841)) Explore Q1M964  Go to UniProtKB:  Q1M964

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VO4 (Subject of Investigation/LOI)	C [auth A]	VANADATE ION O4 V LSGOVYNHVSXFFJ-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
NA	D [auth A], E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DDZ	A	L-PEPTIDE LINKING	C3 H7 N O4		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.162 (Depositor), 0.162 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.135 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.063	α = 90
b = 97.129	β = 90
c = 179.024	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Jonas, S., Hyvonen, M., Hollfelder, F.

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Funding Organization	Location	Grant Number
European Union (EU)	European Union	ENDIRPRO (HPRN-CT-2002-00239)
European Union (EU)	European Union	ProSA (19475)
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/W000504/1

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release