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- PDB-9q27: FphA, Staphylococcus aureus fluorophosphonate-binding serine hydr... -

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Basic information

Entry
Database: PDB / ID: 9q27
TitleFphA, Staphylococcus aureus fluorophosphonate-binding serine hydrolases A, apo form, crystal form 3
ComponentsCarboxylic ester hydrolase
KeywordsHYDROLASE / lipase / esterase / 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: 1.77 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 3
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


Theoretical massNumber of molelcules
Total (without water)52,2371
Polymers52,2371
Non-polymers00
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.168, 55.758, 113.704
Angle α, β, γ (deg.)90.00, 111.43, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-548-

HOH

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Components

#1: Protein Carboxylic ester hydrolase


Mass: 52236.898 Da / Num. of mol.: 1 / 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.: 335 / 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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.3 uL 16.32 mg/mL FphA (10 mM Tris-HCl PH 8.0, 10 mM NaCl) were mixed with 0.15 uL of reservoir solution. Sitting drop reservoir contained 25 uL 0.1 M Tris pH 8.5 and 0.7 M Sodium citrate ...Details: 0.3 uL 16.32 mg/mL FphA (10 mM Tris-HCl PH 8.0, 10 mM NaCl) were mixed with 0.15 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 35 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: 1.77→46.75 Å / Num. obs: 51476 / % possible obs: 97.6 % / Redundancy: 4.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.047 / Rrim(I) all: 0.102 / Χ2: 1.01 / Net I/σ(I): 8.8 / Num. measured all: 240516
Reflection shellResolution: 1.77→1.8 Å / % possible obs: 92.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.93 / Num. measured all: 12566 / Num. unique obs: 2823 / CC1/2: 0.435 / Rpim(I) all: 0.489 / Rrim(I) all: 1.055 / Χ2: 1.12 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Aimless0.8.2data scaling
XDS20241002data reduction
PHASER2.8.3phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→46.75 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 2570 4.99 %
Rwork0.1616 --
obs0.1633 51459 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3673 0 0 335 4008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063887
X-RAY DIFFRACTIONf_angle_d0.7925297
X-RAY DIFFRACTIONf_dihedral_angle_d14.6241436
X-RAY DIFFRACTIONf_chiral_restr0.054558
X-RAY DIFFRACTIONf_plane_restr0.006696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.80.35961410.29852606X-RAY DIFFRACTION93
1.8-1.840.34491260.27472663X-RAY DIFFRACTION96
1.84-1.880.28381360.252636X-RAY DIFFRACTION96
1.88-1.920.24941470.23632715X-RAY DIFFRACTION97
1.92-1.970.2751430.20652668X-RAY DIFFRACTION97
1.97-2.020.21281530.19452661X-RAY DIFFRACTION97
2.02-2.080.21521250.17882706X-RAY DIFFRACTION97
2.08-2.150.20311580.16682690X-RAY DIFFRACTION97
2.15-2.230.18651470.16242711X-RAY DIFFRACTION97
2.23-2.310.21461460.16152723X-RAY DIFFRACTION98
2.31-2.420.19651200.16232722X-RAY DIFFRACTION98
2.42-2.550.19751230.15672758X-RAY DIFFRACTION98
2.55-2.710.19191410.16252737X-RAY DIFFRACTION98
2.71-2.920.18321410.16532745X-RAY DIFFRACTION98
2.92-3.210.21871730.16272729X-RAY DIFFRACTION99
3.21-3.670.19681450.14742777X-RAY DIFFRACTION99
3.67-4.630.13591430.12652796X-RAY DIFFRACTION99
4.63-46.750.17991620.14022846X-RAY DIFFRACTION99

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