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- PDB-9gvd: Structure of phosphonate monoester hydrolase from Rhizobium legum... -

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Basic information

Entry
Database: PDB / ID: 9gvd
TitleStructure of phosphonate monoester hydrolase from Rhizobium leguminosarum with vanadate
ComponentsMultifunctional alkaline phosphatase superfamily protein pRL90232
KeywordsHYDROLASE / Phosphonate monoester hydrolase / promiscuous enzyme
Function / homology
Function and homology information


sulfuric ester hydrolase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / metal ion binding / cytoplasm
Similarity search - Function
: / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
: / VANADATE ION / Multifunctional alkaline phosphatase superfamily protein pRL90232
Similarity search - Component
Biological speciesRhizobium johnstonii 3841 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsJonas, S. / Hyvonen, M. / Hollfelder, F.
Funding supportEuropean Union, United Kingdom, 3items
OrganizationGrant numberCountry
European Union (EU)ENDIRPRO (HPRN-CT-2002-00239)European Union
European Union (EU)ProSA (19475)European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W000504/1 United Kingdom
CitationJournal: To Be Published
Title: Efficient leaving group stabilization and hydrophobic binding make Phosphonate Monoester Hydrolase (PMH) an exceptionally promiscuous enzyme
Authors: Mohamed, M.F. / Jonas, S. / Miton, C. / van Loo, B. / Hyvonen, M. / Hollfelder, F.
History
DepositionSep 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multifunctional alkaline phosphatase superfamily protein pRL90232
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3376
Polymers61,0981
Non-polymers2395
Water13,097727
1
A: Multifunctional alkaline phosphatase superfamily protein pRL90232
hetero molecules

A: Multifunctional alkaline phosphatase superfamily protein pRL90232
hetero molecules

A: Multifunctional alkaline phosphatase superfamily protein pRL90232
hetero molecules

A: Multifunctional alkaline phosphatase superfamily protein pRL90232
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,34924
Polymers244,3944
Non-polymers95520
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area19570 Å2
ΔGint-138 kcal/mol
Surface area66630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.063, 97.129, 179.024
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1085-

HOH

21A-1297-

HOH

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Components

#1: Protein Multifunctional alkaline phosphatase superfamily protein pRL90232 / Phosphodiesterase / Phosphonate monoester hydrolase / RlPMH


Mass: 61098.426 Da / Num. of mol.: 1 / Mutation: C57fGly
Source method: isolated from a genetically manipulated source
Details: C57 becomes posttranslationally modified to formylglycine fGly (DDZ)
Source: (gene. exp.) Rhizobium johnstonii 3841 (bacteria) / Gene: pRL90232 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q1M964, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 727 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M TRIS-HCL PH 8.5, 25% PEG 4000, 0.2M SODIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9738 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9738 Å / Relative weight: 1
ReflectionResolution: 1.2→33.66 Å / Num. obs: 144955 / % possible obs: 88.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 12.92 Å2 / CC1/2: 1 / Rpim(I) all: 0.0253 / Rrim(I) all: 0.066 / Net I/σ(I): 15.17
Reflection shellResolution: 1.2→1.28 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 0.73 / Num. unique obs: 13108 / CC1/2: 0.536 / Rpim(I) all: 0.953 / Rrim(I) all: 1.94 / % possible all: 49.5

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSVERSION Feb 5, 2021data scaling
PHENIX1.21.1_5286phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→33.66 Å / SU ML: 0.1209 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3484
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1622 7226 5 %
Rwork0.1342 137342 -
obs0.1357 144568 87.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.81 Å2
Refinement stepCycle: LAST / Resolution: 1.2→33.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4058 0 9 727 4794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01074252
X-RAY DIFFRACTIONf_angle_d1.15145808
X-RAY DIFFRACTIONf_chiral_restr0.0942610
X-RAY DIFFRACTIONf_plane_restr0.0135776
X-RAY DIFFRACTIONf_dihedral_angle_d13.96941580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.4519870.4811553X-RAY DIFFRACTION30.12
1.21-1.220.4062970.4292145X-RAY DIFFRACTION41
1.22-1.240.3921160.36112482X-RAY DIFFRACTION48.08
1.24-1.250.38341530.3252809X-RAY DIFFRACTION54.33
1.25-1.270.33621720.29753162X-RAY DIFFRACTION61.2
1.27-1.290.3221740.27513504X-RAY DIFFRACTION67.95
1.29-1.310.27661950.25483899X-RAY DIFFRACTION74.42
1.31-1.330.28622010.24064193X-RAY DIFFRACTION81.27
1.33-1.350.27852320.23334552X-RAY DIFFRACTION87.47
1.35-1.370.24562620.22794801X-RAY DIFFRACTION93.24
1.37-1.390.28282520.21115123X-RAY DIFFRACTION98.46
1.39-1.420.24662890.18755111X-RAY DIFFRACTION99.26
1.42-1.440.25522720.15465141X-RAY DIFFRACTION99.34
1.44-1.470.22132540.14025202X-RAY DIFFRACTION99.29
1.47-1.510.19242890.13035124X-RAY DIFFRACTION99.49
1.51-1.540.17112700.12235181X-RAY DIFFRACTION99.42
1.54-1.580.17672850.11665158X-RAY DIFFRACTION99.78
1.58-1.620.16212640.11065188X-RAY DIFFRACTION99.69
1.62-1.670.15892700.10925182X-RAY DIFFRACTION99.8
1.67-1.720.14982360.10415230X-RAY DIFFRACTION99.76
1.72-1.790.142660.10885194X-RAY DIFFRACTION99.87
1.79-1.860.14812920.11415197X-RAY DIFFRACTION99.95
1.86-1.940.16432620.11135249X-RAY DIFFRACTION99.96
1.94-2.040.13062620.11295218X-RAY DIFFRACTION99.91
2.04-2.170.12492750.10795244X-RAY DIFFRACTION99.86
2.17-2.340.14922940.11475232X-RAY DIFFRACTION99.98
2.34-2.580.14143000.12435240X-RAY DIFFRACTION99.93
2.58-2.950.15752890.13785297X-RAY DIFFRACTION99.91
2.95-3.710.15032970.12575301X-RAY DIFFRACTION99.89
3.71-33.660.12863190.1225430X-RAY DIFFRACTION98.78

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