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

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Basic information

Entry
Database: PDB / ID: 9gve
TitleStructure of phosphonate monoester hydrolase from Rhizobium leguminosarum with phenyl phosphonate
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
ACETATE ION / : / phenylphosphonic acid / Multifunctional alkaline phosphatase superfamily protein pRL90232
Similarity search - Component
Biological speciesRhizobium johnstonii 3841 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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)61,4397
Polymers61,0981
Non-polymers3416
Water12,214678
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)245,75828
Polymers244,3944
Non-polymers1,36424
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 area19060 Å2
ΔGint-120 kcal/mol
Surface area65510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.136, 96.473, 179.171
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-1036-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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 is posttranslationally modified to formylglycine (fGly, DDZ)
Source: (gene. exp.) Rhizobium johnstonii 3841 (bacteria) / Gene: pRL90232 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q1M964, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases

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Non-polymers , 5 types, 684 molecules

#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-SV7 / phenylphosphonic acid


Mass: 158.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7O3P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 678 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.13 Å3/Da / Density % sol: 42.16 %
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: 0.9728 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9728 Å / Relative weight: 1
ReflectionResolution: 1.49→48.24 Å / Num. obs: 84122 / % possible obs: 99.2 % / Redundancy: 7.2 % / Biso Wilson estimate: 16.9 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.0601 / Rrim(I) all: 0.161 / Net I/σ(I): 9.89
Reflection shellResolution: 1.49→1.59 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 0.76 / Num. unique obs: 13522 / CC1/2: 0.422 / Rpim(I) all: 1.08 / Rrim(I) all: 2.89 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSVERSION Feb 5, 2021data reduction
PHENIX1.21.1_5286phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→44.34 Å / SU ML: 0.2251 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.7284
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1846 4252 5.07 %
Rwork0.1713 79669 -
obs0.172 83921 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.65 Å2
Refinement stepCycle: LAST / Resolution: 1.49→44.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4051 0 18 678 4747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00644232
X-RAY DIFFRACTIONf_angle_d0.88045774
X-RAY DIFFRACTIONf_chiral_restr0.0875606
X-RAY DIFFRACTIONf_plane_restr0.0087770
X-RAY DIFFRACTIONf_dihedral_angle_d14.4771563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.49611260.50322154X-RAY DIFFRACTION82.28
1.51-1.530.42651320.39332644X-RAY DIFFRACTION99.75
1.53-1.550.4131350.37792628X-RAY DIFFRACTION99.89
1.55-1.570.38381470.34752653X-RAY DIFFRACTION99.89
1.57-1.590.38321480.33332662X-RAY DIFFRACTION100
1.59-1.610.33771280.31582651X-RAY DIFFRACTION99.93
1.61-1.630.31241450.29722678X-RAY DIFFRACTION100
1.63-1.660.29531400.2822627X-RAY DIFFRACTION99.86
1.66-1.680.34181200.26872679X-RAY DIFFRACTION99.89
1.68-1.710.25981270.24482646X-RAY DIFFRACTION99.93
1.71-1.740.25121320.22932671X-RAY DIFFRACTION99.89
1.74-1.770.23421400.22572656X-RAY DIFFRACTION99.96
1.77-1.810.22511390.20462633X-RAY DIFFRACTION99.89
1.81-1.840.24911510.20252661X-RAY DIFFRACTION99.96
1.84-1.880.20581150.19032688X-RAY DIFFRACTION99.96
1.88-1.930.22551510.17462673X-RAY DIFFRACTION99.96
1.93-1.970.1691310.16932665X-RAY DIFFRACTION99.96
1.97-2.030.17741380.16062669X-RAY DIFFRACTION99.96
2.03-2.090.171360.15692681X-RAY DIFFRACTION99.93
2.09-2.150.1661470.15862645X-RAY DIFFRACTION100
2.15-2.230.17641330.15332693X-RAY DIFFRACTION99.89
2.23-2.320.18111520.15012664X-RAY DIFFRACTION99.93
2.32-2.430.17971630.15372658X-RAY DIFFRACTION100
2.43-2.550.18451620.1552661X-RAY DIFFRACTION99.96
2.55-2.710.17311320.1572723X-RAY DIFFRACTION99.96
2.71-2.920.17221570.162683X-RAY DIFFRACTION99.93
2.92-3.220.17121350.14892715X-RAY DIFFRACTION99.69
3.22-3.680.15931620.13182691X-RAY DIFFRACTION99.44
3.68-4.640.10921370.11212739X-RAY DIFFRACTION98.83
4.64-44.340.12531910.1332778X-RAY DIFFRACTION98.12
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0186446491671-0.03666925691440.03586619655480.0709112994705-0.06978837603650.06737597928140.06288991642290.00124353621052-0.0190023378546-0.08236842627660.01098368159050.07223661456870.075320114482-0.037757160330.003686320953760.17553277781-0.0240479041659-0.02256183761140.163152787334-0.00598468323030.17087542334920.233535897815.151119953163.1698361855
20.05859053716730.00613489114481-0.01987780567690.04774967272960.002686515351030.1083504730830.00128495193246-0.01657124173680.0148816710982-0.00287522296870.00150295750654-0.005711872178860.02948885069530.029233246811-1.0041930141E-70.1587980628360.009122778528340.00127817323870.154786400228-0.005619427946390.14703857480133.415240361926.95416121277.8560006453
30.07431967101780.0159644614188-0.0209642300270.229518882006-0.03833522988240.3010903304060.0110343561577-0.0032103545885-0.00693249576431-0.06457493234320.01581815775950.004617975851060.0838969715795-0.00614759154535-5.44654042915E-60.144883591832-0.0048181318217-0.001524616253930.1268250152930.001050107232130.13349169724929.389477746320.417822758265.6559820542
40.1302533997710.01573343660680.08682997817540.106537783798-0.04824478595520.1237192062730.007298772946470.01570878689320.0122179473133-0.08558732244690.02617217029240.005074668380170.023370509171-0.01373945178671.26876173181E-50.178237975793-0.00723660621282.4984051844E-50.1455073914780.00121756441970.14860192985129.118840855542.489748412155.4910769581
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 43 )2 - 431 - 42
22chain 'A' and (resid 44 through 169 )44 - 16943 - 168
33chain 'A' and (resid 170 through 424 )170 - 424169 - 423
44chain 'A' and (resid 425 through 514 )425 - 514424 - 513

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