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- PDB-9c0m: FphH, Staphylococcus aureus fluorophosphonate-binding serine hydr... -

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Basic information

Entry
Database: PDB / ID: 9c0m
TitleFphH, Staphylococcus aureus fluorophosphonate-binding serine hydrolases H, apo form 2 at room temperature
ComponentsAlpha/beta fold hydrolase
KeywordsHYDROLASE / FphH / Staphylococcus aureus / S. aureus / fluorophosphonate-binding / serine hydrolases / lipase / room temperature / humidity / humidifier
Function / homologyEsterase/lipase / : / Serine aminopeptidase, S33 / carboxylesterase / Serine aminopeptidase, S33 / carboxylesterase activity / Alpha/Beta hydrolase fold / Carboxylesterase
Function and homology information
Biological speciesStaphylococcus aureus USA300-CA-263 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.285, 62.285, 164.094
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-435-

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.: 78 / 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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2 uL 12 mg/mL FphH (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 1.5 uL of reservoir solution and 0.5 uL crystals seeds in reservoir solution. Sitting drop reservoir contained 100mM ...Details: 2 uL 12 mg/mL FphH (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 1.5 uL of reservoir solution and 0.5 uL crystals seeds in reservoir solution. Sitting drop reservoir contained 100mM Calcium acetate hydrate, 100mM Tris pH 7.5 and 12.5 % w/v PEG 4000.

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Data collection

DiffractionMean temperature: 295 K / Ambient temp details: Room temperature / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→49.61 Å / Num. obs: 11665 / % possible obs: 98.1 % / Redundancy: 5.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.049 / Rrim(I) all: 0.119 / Χ2: 0.95 / Net I/σ(I): 8 / Num. measured all: 66796
Reflection shellResolution: 2.5→2.6 Å / % possible obs: 86.1 % / Redundancy: 5.1 % / Rmerge(I) obs: 1.19 / Num. measured all: 5779 / Num. unique obs: 1129 / CC1/2: 0.5 / Rpim(I) all: 0.549 / Rrim(I) all: 1.316 / Χ2: 1.15 / 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: 2.5→49.61 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2159 542 4.7 %
Rwork0.1744 --
obs0.1765 11523 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→49.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1950 0 4 78 2032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081996
X-RAY DIFFRACTIONf_angle_d0.8712700
X-RAY DIFFRACTIONf_dihedral_angle_d5.748260
X-RAY DIFFRACTIONf_chiral_restr0.05283
X-RAY DIFFRACTIONf_plane_restr0.008356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.750.3271290.26232507X-RAY DIFFRACTION92
2.75-3.150.32051460.2262738X-RAY DIFFRACTION100
3.15-3.970.20971270.17532768X-RAY DIFFRACTION98
3.97-49.610.17671400.14912968X-RAY DIFFRACTION99
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)
15.18260.1014-0.79786.0604-1.02964.7395-0.02971.08510.3141-0.6972-0.0529-0.1127-0.37070.16840.09950.377-0.01230.00760.6720.10080.33621.7443-9.979416.906
26.90221.6469-0.05965.56211.07987.3526-0.07780.51870.9047-0.120.04550.6251-0.9246-0.5393-0.02210.32550.0508-0.00560.47790.12430.408612.5799-5.415324.3888
33.85031.4254-2.14286.4711-2.11278.67290.28060.39631.1637-0.1113-0.718-0.6142-2.08451.44010.22611.4721-0.10010.19691.2310.54641.454427.366914.18119.7148
46.4239-0.2916-1.41015.3467-0.54975.76240.2422-0.02550.81120.1906-0.09050.0447-0.88910.1169-0.08140.4156-0.03670.02760.36940.05380.38715.482-3.119231.0451
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 85 )
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 124 )
3X-RAY DIFFRACTION3chain 'A' and (resid 125 through 157 )
4X-RAY DIFFRACTION4chain 'A' and (resid 158 through 246 )

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