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- PDB-8tav: FphH, Staphylococcus aureus fluorophosphonate-binding serine hydr... -

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Basic information

Entry
Database: PDB / ID: 8tav
TitleFphH, Staphylococcus aureus fluorophosphonate-binding serine hydrolases H, boronic acid-based compound N34 bound
ComponentsFluorophosphonate-binding serine hydrolase H
KeywordsHYDROLASE / FphH / Staphylococcus aureus / S. aureus / fluorophosphonate-binding / serine hydrolases / lipase / boronic acid / covalent / boron-serine / boron-histidine
Function / homologyBacterial conjugation TrbI-like protein / Type IV secretion system, VirB10 / TraB / TrbI / : / TraB
Function and homology information
Biological speciesStaphylococcus aureus USA300-0114 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsFellner, M.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Capability Build Funding - New Zealand Synchrotron Group Ltd New Zealand
CitationJournal: To Be Published
Title: FphH, Staphylococcus aureus fluorophosphonate-binding serine hydrolases H, boronic acid-based compound N34 bound
Authors: Fellner, M.
History
DepositionJun 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fluorophosphonate-binding serine hydrolase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1249
Polymers28,3361
Non-polymers7888
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.381, 67.381, 55.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Fluorophosphonate-binding serine hydrolase H


Mass: 28335.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus USA300-0114 (bacteria)
Gene: est_2 / Plasmid: F1011 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D6HZA6
#2: Chemical ChemComp-ZKR / [5-(trifluoromethyl)thiophen-2-yl]boronic acid


Mass: 195.955 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H4BF3O2S
Details: There is no H on the B atom as it has reacted with the O from Ser and the N from His.
Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 13uL 10mg/ml FphH (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 5uL N34 (50mM in DMSO) and incubated at RT for ~1 hour. 0.2ul FphH-N34 were mixed with 0.2ul of reservoir solution. Sitting ...Details: 13uL 10mg/ml FphH (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 5uL N34 (50mM in DMSO) and incubated at RT for ~1 hour. 0.2ul FphH-N34 were mixed with 0.2ul of reservoir solution. Sitting drop reservoir contained 180mM Calcium acetate hydrate, 100mM Tris pH 7.5, 9% w/v PEG 8000 and 9% w/v PEG 1000. 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: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.39→47.65 Å / Num. obs: 50414 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.017 / Rrim(I) all: 0.062 / Χ2: 1.04 / Net I/σ(I): 23 / Num. measured all: 682622
Reflection shellResolution: 1.39→1.41 Å / % possible obs: 97.9 % / Redundancy: 12.9 % / Rmerge(I) obs: 1.807 / Num. measured all: 31278 / Num. unique obs: 2430 / CC1/2: 0.64 / Rpim(I) all: 0.516 / Rrim(I) all: 1.88 / Χ2: 0.96 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.8data scaling
XDS20220820data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→47.65 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1825 2494 4.95 %
Rwork0.1603 --
obs0.1614 50356 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.39→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 0 40 227 2207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092084
X-RAY DIFFRACTIONf_angle_d1.1132834
X-RAY DIFFRACTIONf_dihedral_angle_d8.899277
X-RAY DIFFRACTIONf_chiral_restr0.076289
X-RAY DIFFRACTIONf_plane_restr0.008372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.410.33151380.29462584X-RAY DIFFRACTION98
1.41-1.440.28411360.25122634X-RAY DIFFRACTION100
1.44-1.470.2791430.23632665X-RAY DIFFRACTION100
1.47-1.510.2081280.21132654X-RAY DIFFRACTION100
1.51-1.540.21241600.20842612X-RAY DIFFRACTION100
1.54-1.590.18991450.18022677X-RAY DIFFRACTION100
1.59-1.630.19261310.17212623X-RAY DIFFRACTION100
1.63-1.690.19481210.15722691X-RAY DIFFRACTION100
1.69-1.750.20331380.1672654X-RAY DIFFRACTION100
1.75-1.820.17721460.1492647X-RAY DIFFRACTION100
1.82-1.90.17051250.14622670X-RAY DIFFRACTION100
1.9-20.15461380.1422645X-RAY DIFFRACTION100
2-2.120.16571360.14592686X-RAY DIFFRACTION100
2.12-2.290.14631410.13732649X-RAY DIFFRACTION100
2.29-2.520.181410.14692661X-RAY DIFFRACTION100
2.52-2.880.15981360.16142683X-RAY DIFFRACTION100
2.88-3.630.17361440.15552690X-RAY DIFFRACTION100
3.63-47.650.1951470.15772737X-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)
11.5222-0.0288-0.17932.6437-0.33131.3152-0.0268-0.09990.10410.15450.01710.1078-0.1826-0.07150.01210.15490.0089-0.00430.1236-0.02750.1262-24.794-2.3316.234
21.00970.12540.12181.2901-0.06090.993-0.0202-0.04080.04770.0697-0.00460.0859-0.066-0.05550.02120.13870.0114-0.00050.1346-0.01340.128-26.332-8.7654.491
32.01740.5310.8775.37225.05147.7926-0.0196-0.09470.09020.19530.106-0.1427-0.03360.236-0.13230.21890.0111-0.02350.18740.03130.1956-16.457-20.45918.435
42.21430.27421.47011.08720.37272.2909-0.0581-0.1562-0.1748-0.21940.1963-0.05610.0699-0.0636-0.13430.3830.0351-0.06680.3413-0.03730.2736-16.61-23.12229.241
50.9582-0.19330.0981.3736-0.68252.0622-0.0401-0.0066-0.2021-0.08010.04090.0680.7991-0.2475-0.04320.216-0.0193-0.00030.1523-0.00570.1998-27.611-25.6683.2
61.8580.1935-0.01371.87510.38811.5778-0.02360.0695-0.11810.00940.0487-0.17890.08340.174-0.03480.12520.00240.00120.1733-0.0170.1503-13.35-15.728-3.198
72.0896-0.32310.15063.2581-1.56553.5893-0.01170.23620.2527-0.233-0.0895-0.203-0.21220.17580.12530.1469-0.0009-0.00530.1323-0.0190.1421-16.218-2.937-5.74
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 5:27 )A5 - 27
2X-RAY DIFFRACTION2( CHAIN A AND RESID 28:121 )A28 - 121
3X-RAY DIFFRACTION3( CHAIN A AND RESID 122:140 )A122 - 140
4X-RAY DIFFRACTION4( CHAIN A AND RESID 141:158 )A141 - 158
5X-RAY DIFFRACTION5( CHAIN A AND RESID 159:177 )A159 - 177
6X-RAY DIFFRACTION6( CHAIN A AND RESID 178:227 )A178 - 227
7X-RAY DIFFRACTION7( CHAIN A AND RESID 228:245 )A228 - 245

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