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- PDB-5udq: LarE, a sulfur transferase involved in synthesis of the cofactor ... -

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Basic information

Entry
Database: PDB / ID: 5udq
TitleLarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, apo form
ComponentsLactate racemization operon protein LarE
KeywordsTRANSFERASE / Lar / sulfur transferase / LarE / AMPylation / hexamer / trimer / PP-loop / ATP pyrophophatase domain / lactate / lactate racemization / lactate racemase
Function / homology
Function and homology information


pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase / sulfurtransferase activity / lyase activity / ATP binding
Similarity search - Function
Pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase LarE / NAD/GMP synthase / NAD synthase / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
PHOSPHATE ION / Pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsFellner, M. / Desguin, B. / Hausinger, R.P. / Hu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE.
Authors: Fellner, M. / Desguin, B. / Hausinger, R.P. / Hu, J.
History
DepositionDec 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactate racemization operon protein LarE
B: Lactate racemization operon protein LarE
C: Lactate racemization operon protein LarE
D: Lactate racemization operon protein LarE
E: Lactate racemization operon protein LarE
F: Lactate racemization operon protein LarE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,65120
Polymers190,3136
Non-polymers1,33814
Water11,403633
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16640 Å2
ΔGint-231 kcal/mol
Surface area61690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.401, 107.401, 317.042
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11E-448-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 15 or (resid 16...
21(chain B and (resid 2 through 6 or (resid 7...
31(chain C and (resid 2 through 6 or (resid 7...
41(chain D and (resid 2 through 6 or (resid 7...
51(chain E and (resid 2 through 6 or (resid 7...
61(chain F and (resid 2 through 6 or (resid 7...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 15 or (resid 16...A2 - 15
121(chain A and (resid 2 through 15 or (resid 16...A16 - 17
131(chain A and (resid 2 through 15 or (resid 16...A2 - 276
141(chain A and (resid 2 through 15 or (resid 16...A2 - 276
151(chain A and (resid 2 through 15 or (resid 16...A2 - 276
161(chain A and (resid 2 through 15 or (resid 16...A2 - 276
211(chain B and (resid 2 through 6 or (resid 7...B2 - 6
221(chain B and (resid 2 through 6 or (resid 7...B7
231(chain B and (resid 2 through 6 or (resid 7...B2 - 259
241(chain B and (resid 2 through 6 or (resid 7...B2 - 259
251(chain B and (resid 2 through 6 or (resid 7...B2 - 259
261(chain B and (resid 2 through 6 or (resid 7...B2 - 259
311(chain C and (resid 2 through 6 or (resid 7...C2 - 6
321(chain C and (resid 2 through 6 or (resid 7...C7
331(chain C and (resid 2 through 6 or (resid 7...C2 - 259
341(chain C and (resid 2 through 6 or (resid 7...C2 - 259
351(chain C and (resid 2 through 6 or (resid 7...C2 - 259
361(chain C and (resid 2 through 6 or (resid 7...C2 - 259
411(chain D and (resid 2 through 6 or (resid 7...D2 - 6
421(chain D and (resid 2 through 6 or (resid 7...D7
431(chain D and (resid 2 through 6 or (resid 7...D2 - 259
441(chain D and (resid 2 through 6 or (resid 7...D2 - 259
451(chain D and (resid 2 through 6 or (resid 7...D2 - 259
461(chain D and (resid 2 through 6 or (resid 7...D2 - 259
511(chain E and (resid 2 through 6 or (resid 7...E2 - 6
521(chain E and (resid 2 through 6 or (resid 7...E7
531(chain E and (resid 2 through 6 or (resid 7...E2 - 279
541(chain E and (resid 2 through 6 or (resid 7...E2 - 279
551(chain E and (resid 2 through 6 or (resid 7...E2 - 279
561(chain E and (resid 2 through 6 or (resid 7...E2 - 279
611(chain F and (resid 2 through 6 or (resid 7...F2 - 6
621(chain F and (resid 2 through 6 or (resid 7...F7
631(chain F and (resid 2 through 6 or (resid 7...F2 - 260
641(chain F and (resid 2 through 6 or (resid 7...F2 - 260
651(chain F and (resid 2 through 6 or (resid 7...F2 - 260
661(chain F and (resid 2 through 6 or (resid 7...F2 - 260

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Components

#1: Protein
Lactate racemization operon protein LarE


Mass: 31718.766 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1) (bacteria)
Strain: ATCC BAA-793 / NCIMB 8826 / WCFS1 / Gene: larE, lp_0109 / Plasmid: pGIR076 / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic express DE3 / References: UniProt: F9UST4
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 633 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 4 ul ~39 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 4 ul reservoir solution. Hanging drop reservoir contained 100 ul of 37.5% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 ...Details: 4 ul ~39 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 4 ul reservoir solution. Hanging drop reservoir contained 100 ul of 37.5% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 105 mM ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.09→48.03 Å / Num. obs: 110015 / % possible obs: 99.3 % / Redundancy: 6.3 % / Biso Wilson estimate: 35.97 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.09-2.125.40.5760.702194.9
11.43-48.034.80.0370.995186.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.24 Å47.49 Å
Translation8.24 Å47.49 Å

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Processing

Software
NameVersionClassification
Aimless0.5.25data scaling
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→47.489 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 22.32
RfactorNum. reflection% reflection
Rfree0.231 10071 4.86 %
Rwork0.1866 --
obs0.1888 103709 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.94 Å2 / Biso mean: 46.0055 Å2 / Biso min: 19.67 Å2
Refinement stepCycle: final / Resolution: 2.09→47.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11559 0 70 633 12262
Biso mean--50.11 47.22 -
Num. residues----1509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711880
X-RAY DIFFRACTIONf_angle_d0.87416119
X-RAY DIFFRACTIONf_chiral_restr0.0561872
X-RAY DIFFRACTIONf_plane_restr0.0062082
X-RAY DIFFRACTIONf_dihedral_angle_d13.7714200
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6088X-RAY DIFFRACTION10.704TORSIONAL
12B6088X-RAY DIFFRACTION10.704TORSIONAL
13C6088X-RAY DIFFRACTION10.704TORSIONAL
14D6088X-RAY DIFFRACTION10.704TORSIONAL
15E6088X-RAY DIFFRACTION10.704TORSIONAL
16F6088X-RAY DIFFRACTION10.704TORSIONAL
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 (%)
2.087-2.11070.36722950.28625885618088
2.1107-2.13550.30133750.26336528690399
2.1355-2.16160.30263400.249366516991100
2.1616-2.18890.29793470.249266747021100
2.1889-2.21770.2873120.24666676979100
2.2177-2.24810.27333570.244566687025100
2.2481-2.28020.28053180.229666666984100
2.2802-2.31430.24193410.212366597000100
2.3143-2.35040.24823280.212266807008100
2.3504-2.3890.30023000.212167697069100
2.389-2.43010.23982900.210167096999100
2.4301-2.47430.27753720.214466437015100
2.4743-2.52190.2853600.208566266986100
2.5219-2.57340.253100.205366987008100
2.5734-2.62930.28283110.209167487059100
2.6293-2.69050.26764180.205765887006100
2.6905-2.75780.24493580.198866356993100
2.7578-2.83230.25383250.19766663698899
2.8323-2.91570.2453210.19446641696299
2.9157-3.00980.24073260.20216640696699
3.0098-3.11730.26723560.20166570692699
3.1173-3.24210.24343740.1896538691298
3.2421-3.38960.22043290.18236521685098
3.3896-3.56830.22593160.1776527684398
3.5683-3.79170.19013010.16676535683697
3.7917-4.08440.17182910.15066534682597
4.0844-4.49510.19283930.14726444683797
4.4951-5.14490.19753470.14866504685197
5.1449-6.47940.21673500.18266507685798
6.4794-47.50160.21483100.186230654093
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)
17.4717-0.17747.42610.0389-0.15162.1069-0.64010.81380.25541.0170.455-1.144-1.90550.93340.3350.9269-0.1122-0.29010.5413-0.16060.69332.282510.4151-17.4478
24.3723.6365-0.9693.83782.00539.21390.14470.0893-0.08731.77830.1688-0.2169-0.8605-0.2892-0.24160.83960.2249-0.24420.3536-0.14740.394121.42414.3178-15.2973
33.43093.2434-0.24496.8229-4.01323.4340.31710.07780.27160.58140.01381.5291-0.7048-0.4839-0.27310.58150.22970.05070.4087-0.00590.282713.7663-3.9624-16.9021
44.66912.56771.55487.89512.32315.6102-0.2408-0.0542-0.15931.00810.5520.6558-0.74380.0975-0.20041.050.23280.07590.6338-0.09440.399412.4007-5.6105-8.6781
52.2535-0.83140.41946.44831.27665.42550.23550.3761-0.1811-0.9323-0.01770.43750.08340.299-0.18910.33760.0856-0.02280.46950.01840.234115.8543-15.9406-23.2137
67.0761-7.7264-1.73622.2835-0.36993.0974-0.6737-0.83550.42560.12670.8101-0.83180.12090.1172-0.15210.30550.0266-0.08510.5266-0.06870.317418.6602-8.571-26.8645
72.1205-7.36940.00286.0511-2.75296.2935-0.33660.60950.6017-0.1564-0.033-1.14690.87690.57650.68360.4905-0.01610.0030.559-0.21690.75126.0175-4.2534-26.017
84.82374.42381.95096.77520.67023.86550.167-0.5439-0.511.5272-0.2297-1.0632-0.49290.33380.03130.78080.104-0.29170.488-0.09440.639429.58050.4748-11.0247
93.0772-0.19760.32311.1469-0.92795.37080.130.23270.0346-0.2822-0.07780.0975-0.0422-0.1163-0.03840.31040.0636-0.02580.1703-0.02130.257617.7618-29.1832-5.0257
108.937-0.7856-0.72944.068-0.87342.52480.02640.44430.565-0.2314-0.1726-0.7045-0.19160.63150.11170.4764-0.0027-0.03510.43360.07680.38331.5135-32.7-5.2284
111.437-0.3230.6073.1589-3.19275.3513-0.05610.03920.46560.1814-0.2122-0.3035-0.31290.15140.26590.2486-0.0212-0.01960.22970.00790.49869.35642.702321.9784
124.16174.1243-2.09377.5827-6.57288.3887-0.1132-0.16340.43510.40060.2240.3086-0.4486-0.5845-0.0960.22560.0363-0.01210.3429-0.04430.3961-0.7771.012528.6928
130.0695-0.12730.42334.93-3.89233.26830.04270.10120.1526-0.5024-0.08190.08740.31110.09050.04560.3248-0.01110.00290.301-0.01990.45657.5304-4.082216.6599
144.72740.3008-1.5013.40082.55195.5156-0.01810.10360.0937-0.2683-0.04810.15260.0004-0.19540.05590.21650.0023-0.05010.13570.03660.235216.9195-25.101428.0642
157.6053-2.0482-1.21965.85930.92153.7057-0.0443-0.4803-0.18120.1250.13570.4611-0.1604-0.0686-0.07470.3260.04070.02550.20920.04660.148337.768513.946711.5643
166.812-4.42361.93672.6651-1.58243.31930.58720.3728-0.9309-1.0815-0.33810.5340.3593-0.0127-0.16930.41420.0178-0.02830.2393-0.04820.346344.88830.91793.3135
172.07180.4227-2.39986.4248-9.2762.11170.1483-0.9499-0.13210.5051-0.437-1.1030.17840.29810.50040.42480.0006-0.12120.49810.06910.487359.9902-7.705217.975
186.6233-4.73284.7496.3309-2.80867.4306-0.1757-0.6045-0.19220.23590.0171-0.7302-0.0699-0.35850.0530.2729-0.0212-0.02510.2325-0.01950.200755.38464.23313.5453
192.2791-0.8906-1.97974.80492.5631.6498-0.1419-1.2519-0.28530.68530.1138-0.14890.01730.208-0.05030.3916-0.0003-0.00230.42070.05410.250144.513710.650219.4454
203.7815-0.86621.25111.02440.45050.9695-0.1836-0.3536-1.1080.17780.2260.88320.3795-0.0593-0.13360.36220.02020.06120.43020.12030.615831.79231.742613.7023
212.66812.0615-0.1482.9963-0.00551.76770.0603-0.06270.185-0.0073-0.00970.022-0.0611-0.007-0.05010.27190.0433-0.03230.17730.03780.279645.8015-24.237313.8205
222.9749-3.0836-0.49026.63330.3040.9034-0.0852-0.2283-0.15390.08950.20670.15440.29340.0807-0.12830.4856-0.05910.03180.3157-0.01680.234911.7445-69.287534.0103
237.58266.283-5.47637.9164-5.94526.71980.2346-0.92940.44820.4228-0.45880.04210.2241.08990.08930.59080.0785-0.02710.4974-0.06030.410824.6961-71.035935.414
243.4419-5.2329-1.48228.16633.17943.4897-0.2943-0.0716-0.3803-0.03240.25870.17290.42090.48270.02880.4715-0.08030.05820.32470.00410.305812.5669-55.411730.2609
256.32381.1228-0.9853.22510.11934.1835-0.1102-0.0144-0.3335-0.06190.05830.08730.3679-0.12660.05780.2901-0.0239-0.0140.1283-0.00260.221611.1466-42.053422.9074
261.48531.31690.85735.02952.27183.00130.0204-0.0267-0.39510.2612-0.0754-0.44980.9150.3370.04170.57760.12010.05540.33990.02370.389353.6745-65.884326.852
270.81932.25150.33427.64472.89961.3274-0.17240.1749-0.0359-0.10570.08790.0020.43590.17040.09690.53370.0640.0350.32580.03550.305350.1942-62.029919.3443
284.1682-0.32670.59793.0757-0.51774.83540.05890.2221-0.0442-0.2462-0.0802-0.29290.13090.3030.0130.25320.0076-0.03180.17590.03810.298143.6872-39.16821.7839
291.37630.4736-0.54983.8816-1.82242.27370.0480.19330.0119-0.4204-0.03190.37090.1451-0.0779-0.00870.47630.036-0.05290.2136-0.08170.273123.5315-75.7441-4.5573
302.98430.42141.0850.07570.67752.1539-0.09080.09860.38020.16420.11070.0471-0.65690.1147-0.08690.6018-0.00640.04010.3163-0.04670.343223.2638-71.46489.9771
312.7162-0.150.26894.40840.99222.06940.02150.1362-0.3167-0.12250.0140.08580.44070.0409-0.03350.35690.0372-0.03780.17660.01350.282928.0895-46.342-3.7522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 18 )A2 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 42 )A19 - 42
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 58 )A43 - 58
4X-RAY DIFFRACTION4chain 'A' and (resid 59 through 72 )A59 - 72
5X-RAY DIFFRACTION5chain 'A' and (resid 73 through 95 )A73 - 95
6X-RAY DIFFRACTION6chain 'A' and (resid 96 through 115 )A96 - 115
7X-RAY DIFFRACTION7chain 'A' and (resid 116 through 142 )A116 - 142
8X-RAY DIFFRACTION8chain 'A' and (resid 143 through 177 )A143 - 177
9X-RAY DIFFRACTION9chain 'A' and (resid 178 through 245 )A178 - 245
10X-RAY DIFFRACTION10chain 'A' and (resid 246 through 276 )A246 - 276
11X-RAY DIFFRACTION11chain 'B' and (resid 2 through 95 )B2 - 95
12X-RAY DIFFRACTION12chain 'B' and (resid 96 through 115 )B96 - 115
13X-RAY DIFFRACTION13chain 'B' and (resid 116 through 189 )B116 - 189
14X-RAY DIFFRACTION14chain 'B' and (resid 190 through 259 )B190 - 259
15X-RAY DIFFRACTION15chain 'C' and (resid 2 through 42 )C2 - 42
16X-RAY DIFFRACTION16chain 'C' and (resid 43 through 80 )C43 - 80
17X-RAY DIFFRACTION17chain 'C' and (resid 81 through 95 )C81 - 95
18X-RAY DIFFRACTION18chain 'C' and (resid 96 through 115 )C96 - 115
19X-RAY DIFFRACTION19chain 'C' and (resid 116 through 154 )C116 - 154
20X-RAY DIFFRACTION20chain 'C' and (resid 155 through 177 )C155 - 177
21X-RAY DIFFRACTION21chain 'C' and (resid 178 through 259 )C178 - 259
22X-RAY DIFFRACTION22chain 'D' and (resid 2 through 115 )D2 - 115
23X-RAY DIFFRACTION23chain 'D' and (resid 116 through 164 )D116 - 164
24X-RAY DIFFRACTION24chain 'D' and (resid 165 through 189 )D165 - 189
25X-RAY DIFFRACTION25chain 'D' and (resid 190 through 259 )D190 - 259
26X-RAY DIFFRACTION26chain 'E' and (resid 2 through 115 )E2 - 115
27X-RAY DIFFRACTION27chain 'E' and (resid 116 through 189 )E116 - 189
28X-RAY DIFFRACTION28chain 'E' and (resid 190 through 279 )E190 - 279
29X-RAY DIFFRACTION29chain 'F' and (resid 2 through 154 )F2 - 154
30X-RAY DIFFRACTION30chain 'F' and (resid 155 through 177 )F155 - 177
31X-RAY DIFFRACTION31chain 'F' and (resid 178 through 260 )F178 - 260

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