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- PDB-6vh9: FphF, Staphylococcus aureus fluorophosphonate-binding serine hydr... -

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Basic information

Entry
Database: PDB / ID: 6vh9
TitleFphF, Staphylococcus aureus fluorophosphonate-binding serine hydrolases F, apo form
ComponentsEsterase family protein
KeywordsHYDROLASE / FphF / Staphylococcus aureus / S. aureus / fluorophosphonate-binding / serine hydrolases / sodium bound
Function / homology
Function and homology information


S-formylglutathione hydrolase / S-formylglutathione hydrolase activity / formaldehyde catabolic process / cytosol
Similarity search - Function
S-formylglutathione hydrolase / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
S-formylglutathione hydrolase / S-formylglutathione hydrolase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.71 Å
AuthorsFellner, M. / Jamieson, S.A. / Brewster, J.L. / Mace, P.D.
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Structural Basis for the Inhibitor and Substrate Specificity of the Unique Fph Serine Hydrolases of Staphylococcus aureus .
Authors: Fellner, M. / Lentz, C.S. / Jamieson, S.A. / Brewster, J.L. / Chen, L. / Bogyo, M. / Mace, P.D.
History
DepositionJan 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Esterase family protein
B: Esterase family protein
C: Esterase family protein
D: Esterase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,9158
Polymers116,8234
Non-polymers924
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11640 Å2
ΔGint-72 kcal/mol
Surface area33570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.145, 87.145, 453.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -1 through 42 or resid 44...
21(chain B and (resid -1 through 42 or resid 44...
31(chain C and (resid -1 through 42 or resid 44...
41(chain D and (resid -1 through 42 or resid 44...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLEULEU(chain A and (resid -1 through 42 or resid 44...AA-1 - 421 - 44
12LEULEUTYRTYR(chain A and (resid -1 through 42 or resid 44...AA44 - 5546 - 57
13ARGARGILEILE(chain A and (resid -1 through 42 or resid 44...AA57 - 19959 - 201
14CYSCYSILEILE(chain A and (resid -1 through 42 or resid 44...AA201 - 221203 - 223
15VALVALLYSLYS(chain A and (resid -1 through 42 or resid 44...AA223 - 244225 - 246
16ALAALANANA(chain A and (resid -1 through 42 or resid 44...AA - E246 - 501248
21GLYGLYLEULEU(chain B and (resid -1 through 42 or resid 44...BB-1 - 421 - 44
22LEULEUTYRTYR(chain B and (resid -1 through 42 or resid 44...BB44 - 5546 - 57
23ARGARGILEILE(chain B and (resid -1 through 42 or resid 44...BB57 - 19959 - 201
24GLYGLYNANA(chain B and (resid -1 through 42 or resid 44...BB - F-1 - 5011
25VALVALLYSLYS(chain B and (resid -1 through 42 or resid 44...BB223 - 244225 - 246
26ALAALANANA(chain B and (resid -1 through 42 or resid 44...BB - F246 - 501248
31GLYGLYLEULEU(chain C and (resid -1 through 42 or resid 44...CC-1 - 421 - 44
32LEULEUTYRTYR(chain C and (resid -1 through 42 or resid 44...CC44 - 5546 - 57
33ARGARGILEILE(chain C and (resid -1 through 42 or resid 44...CC57 - 19959 - 201
34CYSCYSILEILE(chain C and (resid -1 through 42 or resid 44...CC201 - 221203 - 223
35VALVALLYSLYS(chain C and (resid -1 through 42 or resid 44...CC223 - 244225 - 246
36ALAALAASPASP(chain C and (resid -1 through 42 or resid 44...CC246 - 253248 - 255
37NANANANA(chain C and (resid -1 through 42 or resid 44...CG501
41GLYGLYLEULEU(chain D and (resid -1 through 42 or resid 44...DD-1 - 421 - 44
42LEULEUTYRTYR(chain D and (resid -1 through 42 or resid 44...DD44 - 5546 - 57
43ARGARGILEILE(chain D and (resid -1 through 42 or resid 44...DD57 - 19959 - 201
44GLYGLYASPASP(chain D and (resid -1 through 42 or resid 44...DD-1 - 2531 - 255
45GLYGLYASPASP(chain D and (resid -1 through 42 or resid 44...DD-1 - 2531 - 255
46ALAALAASPASP(chain D and (resid -1 through 42 or resid 44...DD246 - 253248 - 255
47NANANANA(chain D and (resid -1 through 42 or resid 44...DH501

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Components

#1: Protein
Esterase family protein / Putative esterase / Tributyrin esterase


Mass: 29205.822 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: EP54_00010, EQ90_02595, HMPREF3211_01237, NCTC10654_02801, NCTC10702_04070, RK64_00235
Plasmid: M1366 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0D6GS23, UniProt: Q2FUY3*PLUS, S-formylglutathione hydrolase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.13 Å3/Da / Density % sol: 42.2 % / Mosaicity: 0.07 °
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 uL ~8.5 mg/ml FphF (20 mM HEPES pH 7.5, 10 mM NaCl) were mixed with 0.1 uL FphF crystal seeds (in 54.4% Tacsimate pH 7.0, 0.1 M Bis-Tris propane pH 6.5, 8% Polypropylene glycol P 400) ...Details: 0.2 uL ~8.5 mg/ml FphF (20 mM HEPES pH 7.5, 10 mM NaCl) were mixed with 0.1 uL FphF crystal seeds (in 54.4% Tacsimate pH 7.0, 0.1 M Bis-Tris propane pH 6.5, 8% Polypropylene glycol P 400) and 0.2 uL of reservoir solution. Sitting drop reservoir contained 50 uL of 2.8 M Sodium acetate. Crystals were soaked for ~20 seconds in 75% reservoir solution and 25% ethylenglycol prior to freezing in liquid nitrogen

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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: Jul 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.71→49.16 Å / Num. obs: 112281 / % possible obs: 99.9 % / Redundancy: 27.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.025 / Rrim(I) all: 0.13 / Net I/σ(I): 16.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.71-1.7427.23.15514484253320.5810.6053.2151.597.8
9.35-49.1619.60.0411763890010.0090.04255.299.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.28 Å49.16 Å
Translation7.28 Å49.16 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIXdev-3699refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4rgy

4rgy


Resolution: 1.71→43.57 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 21.94
RfactorNum. reflection% reflection
Rfree0.2008 10223 4.89 %
Rwork0.1765 --
obs0.1777 112050 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.55 Å2 / Biso mean: 39.4965 Å2 / Biso min: 18.32 Å2
Refinement stepCycle: final / Resolution: 1.71→43.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8236 0 4 457 8697
Biso mean--42.36 45.11 -
Num. residues----1020
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4674X-RAY DIFFRACTION4.825TORSIONAL
12B4674X-RAY DIFFRACTION4.825TORSIONAL
13C4674X-RAY DIFFRACTION4.825TORSIONAL
14D4674X-RAY DIFFRACTION4.825TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.71-1.730.3423400.31646301664196
1.73-1.750.32193100.295767357045100
1.75-1.770.30853270.278266146941100
1.77-1.790.29013710.283166026973100
1.79-1.810.30773410.276366767017100
1.81-1.840.31073660.272365816947100
1.84-1.860.2763190.249566746993100
1.86-1.890.25963440.242366867030100
1.89-1.920.29822870.230866246911100
1.92-1.950.2713570.228166356992100
1.95-1.990.26072990.224467377036100
1.99-2.020.23093360.199766266962100
2.02-2.060.22143400.194866126952100
2.06-2.10.21513510.197565996950100
2.1-2.150.23093680.195566096977100
2.15-2.20.22443850.185666126997100
2.2-2.260.20473570.174266406997100
2.26-2.320.19783120.175466806992100
2.32-2.380.20263720.17865796951100
2.38-2.460.22013520.182366286980100
2.46-2.550.18543320.181166847016100
2.55-2.650.21933380.18266897027100
2.65-2.770.23142930.17766096902100
2.77-2.920.22213450.173167037048100
2.92-3.10.2023350.17366306965100
3.1-3.340.193650.169266487013100
3.34-3.680.1843500.151365936943100
3.68-4.210.16013170.142666676984100
4.21-5.30.14573640.13666156979100
5.3-43.570.18863500.175966456995100
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)
11.1539-0.02010.3211.703-0.03554.1680.05260.0187-0.1106-0.0486-0.07650.04260.3901-0.08810.01810.1557-0.00160.01280.14510.02340.2059-35.0425.8893-10.2606
21.37981.99390.36447.07481.45254.34210.2732-0.4509-0.21141.0212-0.3098-0.31780.53280.29560.03160.38470.009-0.01690.32590.09150.2544-29.962620.2078.3058
33.30851.63190.04134.5264-2.20234.59530.1366-0.1212-0.4672-0.0694-0.195-0.25170.86050.23970.05620.43680.10120.01010.18620.02650.2834-25.807110.095-3.1294
42.19053.0258-3.08216.2939-3.23958.9664-0.0340.09490.0686-0.15420.29980.1287-0.025-0.2203-0.26540.11160.00920.0180.2087-0.00940.2133-21.247343.0305-9.7334
55.4703-0.9385-4.65675.59023.94459.20390.41740.51690.9709-0.45370.2674-0.6994-1.20221.3275-0.68530.4843-0.22650.05190.59990.05710.4476-10.80656.3316-23.044
62.0994-0.00470.13651.6527-0.2344.06140.0759-0.04250.14260.0148-0.0769-0.0724-0.45980.32240.00540.1776-0.04020.00110.1677-0.02010.1968-23.783651.4516-5.5295
77.68062.05582.53697.2287-1.51813.02370.0063-0.37870.25550.17690.0006-0.1879-0.75210.2424-0.01160.3719-0.07090.03660.2401-0.06380.1676-25.209458.24543.9707
84.55655.14571.1578.89623.00527.49390.2749-0.36090.27520.7476-0.38650.5201-0.0794-0.57690.11670.30850.00850.03910.3351-0.03080.2373-31.063951.176914.0685
99.38281.83782.69693.69431.67745.5973-0.2545-0.43920.53710.34040.13410.0824-1.2321-0.0280.1220.67360.02520.02730.2327-0.01710.2736-31.678365.7386.9807
108.54486.17686.88399.72643.63917.3141-0.3968-0.27341.0478-0.2017-0.24930.5-1.4919-0.30510.65180.67860.07320.08330.3391-0.08550.3198-33.772868.08182.6591
118.65779.0544-2.95539.4784-2.95585.08340.1245-0.05890.90860.1205-0.05750.3641-0.895-0.0086-0.06470.51420.0779-0.04420.2221-0.01550.3534-31.502163.6501-9.0459
120.94440.0102-0.79181.56650.52112.02180.02360.0840.03040.00610.0244-0.09330.01040.4603-0.05180.13650.03410.01020.36430.0340.2538-13.337138.6684-25.236
137.9755-1.01022.15022.9927-0.40793.40250.06871.084-0.518-0.40580.09990.28510.32220.3488-0.16340.32240.05210.06190.5532-0.00310.2963-13.889930.3145-39.8501
143.50920.5006-1.87462.1649-0.23913.6734-0.09080.2418-0.1763-0.2289-0.0353-0.14850.22490.41250.1230.24780.13110.02980.4635-0.02810.2743-6.34126.1453-37.9699
150.20140.15370.63011.5993-0.84653.2069-0.01950.03250.02450.00270.01920.055-0.072-0.21880.00480.12470.0492-0.01490.24550.01960.2368-41.55141.0266-26.7964
163.3873-1.2813-1.2493.20421.03253.39170.11920.57060.5356-0.44050.0614-0.4682-0.50710.0898-0.17560.34230.0557-0.02590.43290.0760.3625-39.225651.54-39.766
172.39140.03771.74572.37910.35425.2499-0.0330.21820.2158-0.3091-0.10010.0799-0.6352-0.38740.13330.32680.1288-0.02850.31870.06140.2718-46.908455.3567-38.3527
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 133 )A-1 - 133
2X-RAY DIFFRACTION2chain 'A' and (resid 134 through 189 )A134 - 189
3X-RAY DIFFRACTION3chain 'A' and (resid 190 through 253 )A190 - 253
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 23 )B-1 - 23
5X-RAY DIFFRACTION5chain 'B' and (resid 24 through 39 )B24 - 39
6X-RAY DIFFRACTION6chain 'B' and (resid 40 through 121 )B40 - 121
7X-RAY DIFFRACTION7chain 'B' and (resid 122 through 149 )B122 - 149
8X-RAY DIFFRACTION8chain 'B' and (resid 150 through 189 )B150 - 189
9X-RAY DIFFRACTION9chain 'B' and (resid 190 through 220 )B190 - 220
10X-RAY DIFFRACTION10chain 'B' and (resid 221 through 235 )B221 - 235
11X-RAY DIFFRACTION11chain 'B' and (resid 236 through 253 )B236 - 253
12X-RAY DIFFRACTION12chain 'C' and (resid -1 through 133 )C-1 - 133
13X-RAY DIFFRACTION13chain 'C' and (resid 134 through 162 )C134 - 162
14X-RAY DIFFRACTION14chain 'C' and (resid 163 through 253 )C163 - 253
15X-RAY DIFFRACTION15chain 'D' and (resid -1 through 133 )D-1 - 133
16X-RAY DIFFRACTION16chain 'D' and (resid 134 through 162 )D134 - 162
17X-RAY DIFFRACTION17chain 'D' and (resid 163 through 253 )D163 - 253

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