9GVE | pdb_00009gve

Structure of phosphonate monoester hydrolase from Rhizobium leguminosarum with phenyl phosphonate

PDB DOI: https://doi.org/10.2210/pdb9GVE/pdb

Classification: HYDROLASE
Organism(s): Rhizobium johnstonii 3841
Expression System: Escherichia coli BL21(DE3)
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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.185 (Depositor), 0.184 (DCC)
R-Value Work:
0.171 (Depositor), 0.171 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 61.44 kDa
Atom Count: 4,787
Modeled Residue Count: 513
Deposited Residue Count: 543
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1M964
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SV7 (Subject of Investigation/LOI) Query on SV7 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	phenylphosphonic acid C₆ H₇ O₃ P QLZHNIAADXEJJP-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MN (Subject of Investigation/LOI) Query on MN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.185 (Depositor), 0.184 (DCC)
R-Value Work: 0.171 (Depositor), 0.171 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.136	α = 90
b = 96.473	β = 90
c = 179.171	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Jonas, S.

Hyvonen, M.

Hollfelder, F.

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