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- PDB-9c0l: FphH, Staphylococcus aureus fluorophosphonate-binding serine hydr... -

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Basic information

Entry
Database: PDB / ID: 9c0l
TitleFphH, Staphylococcus aureus fluorophosphonate-binding serine hydrolases H, apo crystal form 2
ComponentsAlpha/beta fold hydrolase
KeywordsHYDROLASE / FphH / Staphylococcus aureus / S. aureus / fluorophosphonate-binding / serine hydrolases / lipase
Function / homologyEsterase/lipase / : / Serine aminopeptidase, S33 / carboxylesterase / Serine aminopeptidase, S33 / carboxylesterase activity / Alpha/Beta hydrolase fold / Alpha/beta fold hydrolase
Function and homology information
Biological speciesStaphylococcus aureus USA300-CA-263 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsFellner, M.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Capability Build Funding - New Zealand Synchrotron Group Ltd New Zealand
CitationJournal: Proteins / Year: 2025
Title: Similar but Distinct-Biochemical Characterization of the Staphylococcus aureus Serine Hydrolases FphH and FphI.
Authors: Fellner, M. / Randall, G. / Bitac, I.R.C.G. / Warrender, A.K. / Sethi, A. / Jelinek, R. / Kass, I.
History
DepositionMay 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Database references / Category: pdbx_database_related
Revision 1.2Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha/beta fold hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4965
Polymers28,3361
Non-polymers1604
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.898, 60.898, 164.513
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-466-

HOH

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Components

#1: Protein Alpha/beta fold hydrolase


Mass: 28335.621 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 USA300-CA-263 (bacteria)
Gene: est_2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D6HZA6
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.3 uL 9.1 mg/mL FphH (10mM HEPES pH 7.6, 100mM NaCl) were mixed with 0.15 uL of reservoir solution. Sitting drop reservoir contained 200mM Calcium acetate hydrate, 100mM Tris pH 8.5, 25 % ...Details: 0.3 uL 9.1 mg/mL FphH (10mM HEPES pH 7.6, 100mM NaCl) were mixed with 0.15 uL of reservoir solution. Sitting drop reservoir contained 200mM Calcium acetate hydrate, 100mM Tris pH 8.5, 25 % w/v PEG 2000 MME. Crystal was frozen in a solution of ~25% Ethylenglycol, 75% reservoir.

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Data collection

DiffractionMean temperature: 100 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: Apr 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.79→48.94 Å / Num. obs: 30069 / % possible obs: 99.7 % / Redundancy: 19.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.027 / Rrim(I) all: 0.116 / Χ2: 1.01 / Net I/σ(I): 15.5 / Num. measured all: 576148
Reflection shellResolution: 1.79→1.83 Å / % possible obs: 94.7 % / Redundancy: 18.6 % / Rmerge(I) obs: 2.565 / Num. measured all: 30217 / Num. unique obs: 1622 / CC1/2: 0.677 / Rpim(I) all: 0.593 / Rrim(I) all: 2.636 / Χ2: 0.94 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.8data scaling
XDSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→41.66 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2143 1491 4.98 %
Rwork0.1842 --
obs0.1857 29956 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→41.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1959 0 4 145 2108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072014
X-RAY DIFFRACTIONf_angle_d0.8882725
X-RAY DIFFRACTIONf_dihedral_angle_d5.437263
X-RAY DIFFRACTIONf_chiral_restr0.059285
X-RAY DIFFRACTIONf_plane_restr0.006360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.850.34361210.33292428X-RAY DIFFRACTION96
1.85-1.910.30351420.25382529X-RAY DIFFRACTION100
1.91-1.990.2541210.21452542X-RAY DIFFRACTION100
1.99-2.080.2481420.20032544X-RAY DIFFRACTION100
2.08-2.190.23411380.19092570X-RAY DIFFRACTION100
2.19-2.330.19351380.16312558X-RAY DIFFRACTION100
2.33-2.510.2091270.1792583X-RAY DIFFRACTION100
2.51-2.760.23911400.18242592X-RAY DIFFRACTION100
2.76-3.160.21971220.19092639X-RAY DIFFRACTION100
3.16-3.980.2031440.18212657X-RAY DIFFRACTION100
3.98-41.660.19411560.16732823X-RAY DIFFRACTION100
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)
13.2233-0.5638-0.12421.74680.10662.62530.06390.28090.1837-0.2002-0.0072-0.0251-0.2330.0124-0.0540.2501-0.0260.0120.24340.02330.221519.2626-8.400419.2869
22.88990.8296-0.99832.4477-0.76382.46980.06650.35120.8349-0.380.0858-0.172-0.65910.0156-0.13280.6460.01470.06040.36640.10470.58619.844910.430314.1654
33.4138-1.4192-0.69971.7475-0.4932.78320.0574-0.28450.23590.02860.0395-0.1209-0.32770.2222-0.08760.2851-0.07440.00750.2911-0.03310.223118.2412-5.535234.5591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 124 )
2X-RAY DIFFRACTION2chain 'A' and (resid 125 through 177 )
3X-RAY DIFFRACTION3chain 'A' and (resid 178 through 246 )

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