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

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Basic information

Entry
Database: PDB / ID: 6wcx
TitleFphF, Staphylococcus aureus fluorophosphonate-binding serine hydrolases F, substrate bound
ComponentsEsterase family protein
KeywordsHYDROLASE / FphF / fluorophosphonate-binding / serine hydrolases / heptanoate / heptan-1-ol
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
HEPTAN-1-OL / S-formylglutathione hydrolase / S-formylglutathione hydrolase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.89 Å
AuthorsFellner, M. / 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
DepositionMar 31, 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 18, 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)117,2888
Polymers116,8234
Non-polymers4654
Water30617
1
A: Esterase family protein
D: Esterase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6444
Polymers58,4122
Non-polymers2322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-22 kcal/mol
Surface area20120 Å2
MethodPISA
2
B: Esterase family protein
C: Esterase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6444
Polymers58,4122
Non-polymers2322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-22 kcal/mol
Surface area20100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.957, 86.957, 454.712
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

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 26 or (resid 27...
31(chain C and (resid -1 through 26 or (resid 27...
41(chain D and (resid -1 through 26 or (resid 27...

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
13ARGARGLYSLYS(chain A and (resid -1 through 42 or resid 44...AA57 - 11059 - 112
14LYSLYSLYSLYS(chain A and (resid -1 through 42 or resid 44...AA111113
15GLYGLYHE4HE4(chain A and (resid -1 through 42 or resid 44...AA - E-1 - 3011
16GLYGLYHE4HE4(chain A and (resid -1 through 42 or resid 44...AA - E-1 - 3011
17GLYGLYHE4HE4(chain A and (resid -1 through 42 or resid 44...AA - E-1 - 3011
18GLYGLYHE4HE4(chain A and (resid -1 through 42 or resid 44...AA - E-1 - 3011
21GLYGLYASPASP(chain B and (resid -1 through 26 or (resid 27...BB-1 - 261 - 28
22GLNGLNGLNGLN(chain B and (resid -1 through 26 or (resid 27...BB2729
23GLYGLYHE4HE4(chain B and (resid -1 through 26 or (resid 27...BB - F-1 - 3011
24GLYGLYHE4HE4(chain B and (resid -1 through 26 or (resid 27...BB - F-1 - 3011
25GLYGLYHE4HE4(chain B and (resid -1 through 26 or (resid 27...BB - F-1 - 3011
26GLYGLYHE4HE4(chain B and (resid -1 through 26 or (resid 27...BB - F-1 - 3011
31GLYGLYASPASP(chain C and (resid -1 through 26 or (resid 27...CC-1 - 261 - 28
32GLNGLNGLNGLN(chain C and (resid -1 through 26 or (resid 27...CC2729
33GLYGLYASPASP(chain C and (resid -1 through 26 or (resid 27...CC-1 - 2531 - 255
34GLYGLYASPASP(chain C and (resid -1 through 26 or (resid 27...CC-1 - 2531 - 255
35GLYGLYASPASP(chain C and (resid -1 through 26 or (resid 27...CC-1 - 2531 - 255
36GLYGLYASPASP(chain C and (resid -1 through 26 or (resid 27...CC-1 - 2531 - 255
41GLYGLYASPASP(chain D and (resid -1 through 26 or (resid 27...DD-1 - 261 - 28
42GLNGLNGLNGLN(chain D and (resid -1 through 26 or (resid 27...DD2729
43GLYGLYASPASP(chain D and (resid -1 through 26 or (resid 27...DD-1 - 2531 - 255
44GLYGLYASPASP(chain D and (resid -1 through 26 or (resid 27...DD-1 - 2531 - 255
45GLYGLYASPASP(chain D and (resid -1 through 26 or (resid 27...DD-1 - 2531 - 255
46GLYGLYASPASP(chain D and (resid -1 through 26 or (resid 27...DD-1 - 2531 - 255

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Components

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


Mass: 29205.822 Da / Num. of mol.: 4 / Mutation: N-terminal GPG from expression tag
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-HE4 / HEPTAN-1-OL


Mass: 116.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H16O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.12 Å3/Da / Density % sol: 42.09 % / Mosaicity: 0.35 °
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.4 uL ~8.0 mg/mL FphF (10 mM HEPES pH 7.5, 10 mM NaCl) were mixed with 0.07 uL ligand solution (~0.5 mM 4-Methylumbelliferyl heptanoate in 100% DMSO) and 0.4 uL of reservoir solution. ...Details: 0.4 uL ~8.0 mg/mL FphF (10 mM HEPES pH 7.5, 10 mM NaCl) were mixed with 0.07 uL ligand solution (~0.5 mM 4-Methylumbelliferyl heptanoate in 100% DMSO) and 0.4 uL of reservoir solution. Sitting drop reservoir contained 50 uL of 0.8 M Sodium formate, 0.1 M Tris pH 7.5, 10 % w/v PEG 8000 and 10 % w/v PEG 1000. Crystals were soaked for ~15 seconds in 75% reservoir solution and 25% glycerol 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: MX1 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.89→49.19 Å / Num. obs: 23922 / % possible obs: 99.4 % / Redundancy: 9.1 % / CC1/2: 0.988 / Rmerge(I) obs: 0.223 / Rpim(I) all: 0.069 / Rrim(I) all: 0.235 / Net I/σ(I): 7.7
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
2.89-3.077.21.1372625236410.5240.381.2131.697.4
8.68-49.1914.80.1071597710820.9950.0290.11226.899.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.28 Å49.19 Å
Translation7.28 Å49.19 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.18rc1-3769refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VH9

6vh9


Resolution: 2.89→49.19 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 24.83
RfactorNum. reflection% reflection
Rfree0.2606 2067 4.96 %
Rwork0.2253 --
obs0.2271 23797 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.41 Å2 / Biso mean: 43.9473 Å2 / Biso min: 23.97 Å2
Refinement stepCycle: final / Resolution: 2.89→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8152 0 32 17 8201
Biso mean--42.39 35.96 -
Num. residues----1020
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4548X-RAY DIFFRACTION8.205TORSIONAL
12B4548X-RAY DIFFRACTION8.205TORSIONAL
13C4548X-RAY DIFFRACTION8.205TORSIONAL
14D4548X-RAY DIFFRACTION8.205TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.89-2.960.27161170.30482397251490
2.96-3.040.31861170.2992608272595
3.04-3.120.34831390.29762620275995
3.12-3.210.31191640.29272572273696
3.21-3.310.30061300.27062580271096
3.31-3.430.2821380.25332631276997
3.43-3.570.33221210.22182616273796
3.57-3.730.2511440.21542673281798
3.73-3.930.26421330.20272711284499
3.93-4.170.20771570.18962678283598
4.17-4.490.18391510.1632648279999
4.5-4.950.22541250.16842713283899
4.95-5.660.20571410.181827342875100
5.66-7.130.24081590.224727072866100
7.13-49.190.31781310.26342704283599
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)
10.5520.46510.42920.42740.14611.3715-0.0583-0.09860.0045-0.07750.0006-0.15820.12760.14860.04640.29150.11660.03860.37060.0610.4584-35.509333.5248-11.7112
20.5831-0.49050.63441.9194-2.79884.0935-0.0571-0.2276-0.4941-0.0242-0.0143-0.09540.6286-0.18020.06480.80510.02230.20690.36740.11140.5517-44.566623.317-28.1503
30.6409-0.23020.20490.80810.30331.1287-0.02880.0455-0.07610.11910.0809-0.03990.62390.469-0.05760.51330.26350.09380.46170.19040.422-26.955623.8965-13.005
40.83580.32780.44610.89970.27342.17410.1232-0.1073-0.0920.2442-0.08660.13690.5135-0.0276-0.03940.36610.00770.02740.33170.09820.2806-36.616924.4213-4.1004
51.7376-0.25510.68052.0470.85691.57160.1367-0.20550.06140.0786-0.0008-0.32390.64070.3344-0.12220.42760.07190.02580.54880.15060.3355-27.058820.76963.8653
63.02152.8223-3.16256.5933-3.54373.3999-0.1571-0.5054-0.1010.6514-0.0929-0.30320.08010.15080.23510.5964-0.0896-0.08970.550.0690.3637-30.421224.07915.1443
71.8922-0.135-0.73432.2620.03882.8931-0.2822-0.4864-0.53750.2411-0.0532-0.26261.08240.19380.32860.70410.0736-0.00490.3750.1180.3897-29.25399.18924.2218
81.85440.6434-0.05262.5106-1.00041.98750.2895-0.0297-0.57260.2214-0.1771-0.31540.59190.389-0.08780.50670.0781-0.00920.36830.07180.3896-24.273411.4039-8.7213
91.76490.2513-0.8092.60810.162.76090.00420.3021-0.2464-0.3023-0.099-0.6058-0.30980.45850.10030.20170.0029-0.00460.47840.0430.3664-16.76648.513-15.0326
101.1229-0.33860.35291.105-0.40963.55840.028-0.0575-0.08090.0473-0.106-0.1483-0.450.57550.04210.1879-0.0453-0.01930.35910.04490.2771-23.761851.5733-4.1949
110.80160.10481.28592.66230.61532.11070.0737-0.12430.05610.1730.1190.1190.1101-0.2523-0.18780.26080.03330.0650.34570.03760.2464-28.982753.428711.028
122.43880.1431.16142.48241.15644.2635-0.0537-0.36030.43830.2391-0.11770.1507-0.9164-0.49610.18430.55190.07740.0290.3674-0.03090.3787-31.94665.25531.456
131.66750.7023-0.44070.70210.07561.17770.1353-0.5211-0.0450.260.007-0.0119-0.08410.5732-0.10440.22490.0606-0.0120.7009-0.05260.4555-13.637843.0879-17.1989
140.5226-0.09570.0350.11810.1090.55750.0493-0.15010.0036-0.01210.2094-0.1068-0.07910.7368-0.16330.04710.28510.06460.98160.050.3736-12.18935.985-29.1858
156.9571-2.33121.31461.5285-0.08780.41980.0860.1241-0.5622-0.1225-0.20540.18180.27161.24680.13380.34870.16590.03630.95290.02680.3934-13.863731.8343-47.6272
161.75920.1348-1.02980.8655-0.07281.4464-0.1008-0.1189-0.25660.16360.1423-0.13450.07750.0391-0.06490.43570.31980.00310.8855-0.00870.3801-5.478522.4216-34.1816
170.13350.16330.08510.4457-0.22630.8253-0.02970.0413-0.01730.08670.0027-0.07840.03480.01150.0190.2360.1221-0.00710.45960.0560.405-41.316340.93-26.827
182.7082-0.47571.09451.29670.30091.6709-0.06510.17520.2565-0.1576-0.0978-0.0156-0.3685-0.27020.15020.3650.13810.07020.37650.09930.3652-40.068450.126-44.4771
191.65020.09951.07480.69670.2091.7082-0.1340.16650.237-0.15750.09740.2307-0.4678-0.33620.05830.47050.1982-0.04670.51180.08610.4557-48.628357.9522-33.8507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 24 )A-1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 39 )A25 - 39
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 68 )A40 - 68
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 133 )A69 - 133
5X-RAY DIFFRACTION5chain 'A' and (resid 134 through 162 )A134 - 162
6X-RAY DIFFRACTION6chain 'A' and (resid 163 through 179 )A163 - 179
7X-RAY DIFFRACTION7chain 'A' and (resid 180 through 221 )A180 - 221
8X-RAY DIFFRACTION8chain 'A' and (resid 222 through 253 )A222 - 253
9X-RAY DIFFRACTION9chain 'B' and (resid -1 through 40 )B-1 - 40
10X-RAY DIFFRACTION10chain 'B' and (resid 41 through 133 )B41 - 133
11X-RAY DIFFRACTION11chain 'B' and (resid 134 through 189 )B134 - 189
12X-RAY DIFFRACTION12chain 'B' and (resid 190 through 253 )B190 - 253
13X-RAY DIFFRACTION13chain 'C' and (resid -1 through 40 )C-1 - 40
14X-RAY DIFFRACTION14chain 'C' and (resid 41 through 146 )C41 - 146
15X-RAY DIFFRACTION15chain 'C' and (resid 147 through 189 )C147 - 189
16X-RAY DIFFRACTION16chain 'C' and (resid 190 through 253 )C190 - 253
17X-RAY DIFFRACTION17chain 'D' and (resid -1 through 133 )D-1 - 133
18X-RAY DIFFRACTION18chain 'D' and (resid 134 through 189 )D134 - 189
19X-RAY DIFFRACTION19chain 'D' and (resid 190 through 253 )D190 - 253

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