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- PDB-9q21: FphA, Staphylococcus aureus fluorophosphonate-binding serine hydr... -

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Basic information

Entry
Database: PDB / ID: 9q21
TitleFphA, Staphylococcus aureus fluorophosphonate-binding serine hydrolases A, apo form, crystal form 2
ComponentsCarboxylic ester hydrolase
KeywordsHYDROLASE / lipase / serine hydrolase / S. aureus / carboxyesterase
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity
Similarity search - Function
Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Carboxylic ester hydrolase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus USA300 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYou, X. / Fellner, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: FphA, Staphylococcus aureus fluorophosphonate-binding serine hydrolases A, apo form, crystal form 2
Authors: You, X. / Fellner, M.
History
DepositionAug 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxylic ester hydrolase
B: Carboxylic ester hydrolase


Theoretical massNumber of molelcules
Total (without water)104,4742
Polymers104,4742
Non-polymers00
Water11,259625
1
A: Carboxylic ester hydrolase


Theoretical massNumber of molelcules
Total (without water)52,2371
Polymers52,2371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carboxylic ester hydrolase


Theoretical massNumber of molelcules
Total (without water)52,2371
Polymers52,2371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.506, 56.192, 117.063
Angle α, β, γ (deg.)90.00, 109.16, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-771-

HOH

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Components

#1: Protein Carboxylic ester hydrolase


Mass: 52236.898 Da / Num. of mol.: 2 / Mutation: N terminal GPG from expression tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus USA300 (bacteria)
Gene: pnbA, SAUSA300_2396 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0H2XHF0, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 uL 16 mg/mL FphA (10 mM Tris-HCl PH 8.0, 10 mM NaCl) were mixed with 0.2 uL of reservoir solution. Sitting drop reservoir contained 25 uL 0.1 M Tris pH 8.5 and 0.7 M Sodium citrate ...Details: 0.2 uL 16 mg/mL FphA (10 mM Tris-HCl PH 8.0, 10 mM NaCl) were mixed with 0.2 uL of reservoir solution. Sitting drop reservoir contained 25 uL 0.1 M Tris pH 8.5 and 0.7 M Sodium citrate tribasic dihydrate. Crystal appeared after 41 days at 16C and grew larger for another month when it was frozen in a solution of ~25% glycerol, 75% reservoir.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 25, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.6→45.8 Å / Num. obs: 135218 / % possible obs: 99.2 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.056 / Rrim(I) all: 0.122 / Χ2: 1.02 / Net I/σ(I): 9.3 / Num. measured all: 632325
Reflection shellResolution: 1.6→1.62 Å / % possible obs: 95.2 % / Redundancy: 4.6 % / Rmerge(I) obs: 1.053 / Num. measured all: 29581 / Num. unique obs: 6421 / CC1/2: 0.253 / Rpim(I) all: 0.541 / Rrim(I) all: 1.19 / Χ2: 0.88 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Aimless0.8.2data scaling
XDSJun 30, 2024data reduction
PHASER2.8.3phasing
PDB_EXTRACT4.3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→41.61 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2012 6884 5.09 %
Rwork0.1781 --
obs0.1793 135142 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→41.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7368 0 0 625 7993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067910
X-RAY DIFFRACTIONf_angle_d0.78710782
X-RAY DIFFRACTIONf_dihedral_angle_d15.7282945
X-RAY DIFFRACTIONf_chiral_restr0.0541129
X-RAY DIFFRACTIONf_plane_restr0.0071423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.610.36092220.34233942X-RAY DIFFRACTION93
1.61-1.630.35742060.32684334X-RAY DIFFRACTION100
1.63-1.650.3352050.31474323X-RAY DIFFRACTION100
1.65-1.670.3452190.30634226X-RAY DIFFRACTION100
1.67-1.70.30542390.29484297X-RAY DIFFRACTION100
1.7-1.720.3182310.28064272X-RAY DIFFRACTION100
1.72-1.740.29492490.26984257X-RAY DIFFRACTION100
1.74-1.770.27532180.25974283X-RAY DIFFRACTION100
1.77-1.80.27692420.24664303X-RAY DIFFRACTION100
1.8-1.830.27452070.23384306X-RAY DIFFRACTION100
1.83-1.860.25682280.22364263X-RAY DIFFRACTION100
1.86-1.890.25542270.20954285X-RAY DIFFRACTION100
1.89-1.930.24562320.19634285X-RAY DIFFRACTION100
1.93-1.970.22252390.18844271X-RAY DIFFRACTION100
1.97-2.010.22822390.1794356X-RAY DIFFRACTION100
2.01-2.060.19732450.17824233X-RAY DIFFRACTION100
2.06-2.110.20582280.16594263X-RAY DIFFRACTION100
2.11-2.160.19612310.16264352X-RAY DIFFRACTION100
2.16-2.230.18142490.16274258X-RAY DIFFRACTION100
2.23-2.30.20262120.16754288X-RAY DIFFRACTION100
2.3-2.380.19532540.17034291X-RAY DIFFRACTION100
2.38-2.480.20652190.16824307X-RAY DIFFRACTION100
2.48-2.590.21522210.17534315X-RAY DIFFRACTION99
2.59-2.730.19062390.17414278X-RAY DIFFRACTION100
2.73-2.90.18632290.16774305X-RAY DIFFRACTION99
2.9-3.120.1942240.15654359X-RAY DIFFRACTION99
3.12-3.440.1662370.14524232X-RAY DIFFRACTION98
3.44-3.930.14672280.1294277X-RAY DIFFRACTION98
3.93-4.950.13722490.12714221X-RAY DIFFRACTION97
4.95-41.610.18612160.18094276X-RAY DIFFRACTION95

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