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- PDB-4ihg: Chasing Acyl Carrier Protein Through a Catalytic Cycle of Lipid A... -

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Basic information

Entry
Database: PDB / ID: 4ihg
TitleChasing Acyl Carrier Protein Through a Catalytic Cycle of Lipid A Production
Components
  • Acyl carrier protein
  • UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
KeywordsTRANSFERASE/LIPID BINDING PROTEIN / Left Handed Beta Helix / LpxD / acyltransferase / Lipid A / Protein-Protein complex / ACP Recognition Domain / ACP mediated product release / TRANSFERASE-LIPID BINDING PROTEIN complex
Function / homology
Function and homology information


UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase activity / UDP-3-O-(3-hydroxyacyl)glucosamine N-acyltransferase / N-acyltransferase activity / lipid A biosynthetic process / response to antibiotic / identical protein binding / cytosol / cytoplasm
Similarity search - Function
UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase LpxD / UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, non-repeat region / UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD / MurE/MurF, N-terminal domain / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 ...UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase LpxD / UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, non-repeat region / UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD / MurE/MurF, N-terminal domain / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
3-HYDROXY-TETRADECANOIC ACID / 4'-PHOSPHOPANTETHEINE / : / UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.89 Å
AuthorsMasoudi, A. / Raetz, C.R.H. / Pemble, C.W.
CitationJournal: Nature / Year: 2014
Title: Chasing acyl carrier protein through a catalytic cycle of lipid A production.
Authors: Masoudi, A. / Raetz, C.R. / Zhou, P. / Pemble, C.W.
History
DepositionDec 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Jan 29, 2014Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
B: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
C: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
D: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
E: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
F: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
G: Acyl carrier protein
H: Acyl carrier protein
I: Acyl carrier protein
J: Acyl carrier protein
K: Acyl carrier protein
L: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,91726
Polymers274,81212
Non-polymers4,10514
Water2,576143
1
A: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
B: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
C: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
G: Acyl carrier protein
H: Acyl carrier protein
I: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,45813
Polymers137,4066
Non-polymers2,0537
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26270 Å2
ΔGint-169 kcal/mol
Surface area45510 Å2
MethodPISA
2
D: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
E: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
F: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
J: Acyl carrier protein
K: Acyl carrier protein
L: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,45813
Polymers137,4066
Non-polymers2,0537
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26220 Å2
ΔGint-180 kcal/mol
Surface area43910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.180, 89.310, 111.933
Angle α, β, γ (deg.)104.09, 92.58, 118.64
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase / UDP-3-O-(3-OHC14)-GlcN N-acyltransferase / Protein FirA / Rifampicin resistance protein


Mass: 36931.277 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: lpxD, firA, omsA, b0179, JW0174 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)/pLysS
References: UniProt: P21645, UDP-3-O-(3-hydroxyacyl)glucosamine N-acyltransferase
#2: Protein
Acyl carrier protein / ACP


Mass: 8870.685 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 'clone D i14' / Gene: acpP, i14_1248 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: G7RM21
#3: Chemical
ChemComp-FTT / 3-HYDROXY-TETRADECANOIC ACID / 3-HYDROXY-MYRISTIC ACID


Mass: 244.370 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H28O3
#4: Chemical
ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 288 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M MES pH 6.5, 0.2 M ammonium sulfate, 20% PEG 8000, vapor diffusion, temperature 288K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. all: 60756 / Num. obs: 59734 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.087 / Χ2: 0.773 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-2.953.70.1927710.749191.1
2.95-33.70.18628680.733194.5
3-3.063.80.18229520.761196.9
3.06-3.123.90.16229700.737198.1
3.12-3.193.90.16230300.758198.8
3.19-3.2740.15529750.766198.8
3.27-3.3540.13729800.794199
3.35-3.4440.11530170.764199
3.44-3.5440.10930210.819198.9
3.54-3.6540.10530050.836199.2
3.65-3.7840.09429860.836199
3.78-3.9440.08630100.865199.2
3.94-4.1140.07830180.885199.4
4.11-4.3340.07430230.862199.3
4.33-4.640.06330270.779199.4
4.6-4.9640.06230390.772199.5
4.96-5.4640.07230000.757199.5
5.46-6.2440.06430560.708199.7
6.24-7.8640.04930080.653199.7
7.86-5040.03129780.611197.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXdev_1232refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→28.433 Å / Occupancy max: 1 / Occupancy min: 0.09 / FOM work R set: 0.8064 / SU ML: 0.32 / σ(F): 0.18 / Phase error: 26.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2529 1899 3.3 %Random automatically determined by Phenix
Rwork0.2042 ---
obs0.2059 57571 94.51 %-
all-59470 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.31 Å2 / Biso mean: 49.4668 Å2 / Biso min: 17.1 Å2
Refinement stepCycle: LAST / Resolution: 2.89→28.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17319 0 262 143 17724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00517782
X-RAY DIFFRACTIONf_angle_d0.9724070
X-RAY DIFFRACTIONf_chiral_restr0.0392862
X-RAY DIFFRACTIONf_plane_restr0.0043124
X-RAY DIFFRACTIONf_dihedral_angle_d13.4336542
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.89-2.96320.28341100.23243327343779
2.9632-3.04320.30091430.23513707385088
3.0432-3.13260.33971130.23213858397192
3.1326-3.23360.30791460.24393923406993
3.2336-3.3490.30351310.23453951408294
3.349-3.48290.25371350.21924036417195
3.4829-3.64110.26971380.21884045418396
3.6411-3.83260.27361360.20694109424597
3.8326-4.07210.22351450.19434073421897
4.0721-4.38550.221380.17734115425398
4.3855-4.82490.2171380.16234101423998
4.8249-5.51860.24261410.18874161430298
5.5186-6.93610.23961440.20924135427998
6.9361-28.43440.2041410.18624131427298
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)
11.23371.7775-0.09922.78780.15223.01160.0697-0.14820.0748-0.0751-0.0664-0.0055-0.0967-0.02240.00010.4283-0.0553-0.03260.2713-0.00070.2728-18.41524.228285.3402
20.46380.4179-0.10440.5507-0.07012.52650.0262-0.00240.01450.1216-0.070.0067-0.28340.18280.00510.23490.0080.00160.19550.00340.2803-14.407517.514754.8766
30.39590.79060.46651.10440.44223.39580.10040.0138-0.2118-0.10310.0865-0.04031.0282-0.28570.02380.6581-0.0006-0.01460.23820.00750.3571-22.3817-14.782538.6122
41.3454-0.04860.24540.7648-0.23462.2175-0.0205-0.00140.04960.1075-0.08240.09370.1115-0.4924-0.00830.21270.00180.02970.2777-0.01930.2567-29.96327.984655.9171
51.34340.7732-0.41992.2776-0.77222.5829-0.03630.07070.2851-0.17650.0553-0.0481-0.51210.43020.00170.308-0.10860.02030.4739-0.0350.312-1.904724.522831.7537
60.6927-0.26150.31741.3330.10162.0033-0.09940.00460.0115-0.06270.0130.16830.0831-0.2387-0.00910.1937-0.0139-0.0310.2476-0.00170.2482-26.720210.309738.0803
70.39910.25690.46451.5491-0.00121.2452-0.34080.51390.1593-1.01810.25820.8708-0.3584-0.61290.12161.3163-0.3155-0.35340.70580.10460.5421-43.659110.5158-48.8387
80.53050.79390.0031.7174-0.71181.3097-0.06920.169-0.1393-0.33540.1077-0.10490.4247-0.14150.00060.5157-0.0955-0.00540.3127-0.01020.3191-30.0966-10.728-21.2362
90.119-0.03890.14520.1015-0.0820.36250.2921-0.2191-0.0009-0.2760.07160.33120.7169-0.19470.00420.5293-0.2243-0.08740.55030.01580.5202-48.5465-6.3175-17.484
100.18150.16610.11821.1287-0.86990.7504-0.0246-0.17890.16380.04440.03530.55740.1527-1.013-0.00350.3558-0.0967-0.00660.97920.04810.5826-58.14576.8128-7.6461
110.19620.7059-0.03171.414-0.03763.1940.1-0.01770.0268-0.0358-0.0878-0.1511-0.80520.1904-0.00180.3179-0.0191-0.0150.31630.02570.3667-15.261722.283-4.7779
120.66560.2203-0.05091.4608-0.12741.4057-0.09250.02540.1246-0.21360.12590.34040.0303-0.55780.02440.2769-0.0129-0.06090.44260.04940.3669-41.187513.2243-17.922
130.66521.5177-0.20292.4679-0.69690.8650.1198-0.23-0.08290.1622-0.0792-0.15970.3957-0.071500.6544-0.0831-0.03830.3698-0.00150.3682-35.7228-27.4226-0.6985
140.13870.4772-0.29981.4097-0.231.55960.0619-0.074-0.04550.1149-0.0772-0.12450.2166-0.0227-00.2893-0.0114-0.03790.2876-0.0030.2752-23.34522.6623-2.6984
150.76260.8541-0.3381.1627-0.07010.9599-0.0719-0.18360.34330.20940.01130.6284-0.1562-1.0814-0.00320.2680.09860.03460.8258-0.00540.5676-54.736610.475-1.367
160.06680.1141-0.09990.2557-0.32680.5951-0.86560.3289-0.91160.0724-0.33470.39110.40130.1812-0.01991.2350.05490.22390.6773-0.1620.792-58.364117.19473.5259
170.51830.3134-0.33040.2789-0.12530.2014-0.7523-0.1120.72080.42320.4055-0.84370.19870.2744-0.00680.82320.25020.10690.8904-0.16910.8265-48.461721.722368.8163
180.06720.0698-0.00030.05820.0107-0.00620.6454-0.0930.62250.0540.5633-0.5724-0.32260.6680.00130.89120.07120.14990.9854-0.28911.1603-48.77827.270876.0824
190.0148-0.0024-0.03330.00790.02480.07270.35530.1451-0.1414-0.343-0.1010.4168-0.2772-0.0481-0.00020.9471-0.1474-0.19711.38850.12860.9075-59.543412.959427.5567
200.0162-0.0364-0.03440.05150.05360.041-0.2310.4066-0.1777-0.7999-0.4459-0.08450.23880.1581-0.00090.8439-0.1053-0.10711.3858-0.29560.9201-54.76083.809626.9889
210.20140.150.13480.16120.01060.1908-0.34050.30190.90830.0470.36490.2694-0.2593-0.3769-0.00020.4060.0872-0.07990.9530.04640.7673-56.631714.478437.9406
220.1211-0.1099-0.01190.1146-0.03090.0330.05290.1758-0.0148-0.0960.49150.27890.3863-0.3708-0.00050.52460.0119-0.07150.9619-0.06071.0518-63.27216.93838.7081
230.0279-0.010.04150.0577-0.0120.04010.1893-0.05990.3610.24110.24970.3564-0.8487-0.42120.00040.96240.3295-0.14381.4692-0.12251.198-34.984548.970448.1196
240.02010.03410.04210.22960.09380.1116-0.09640.65121.3299-0.42680.31290.2826-0.3053-0.47810.00010.97540.26460.03380.90750.06351.181-37.641644.409241.416
250.04130.055-0.00360.05010.0020.0160.67390.08110.3899-0.4694-0.50960.3114-0.3463-0.48080.00010.74590.0355-0.06491.0681-0.24571.2576-71.995728.852-25.6046
260.4518-0.13560.06080.2480.28370.39470.2819-0.05040.2312-0.3555-0.31980.5352-0.2327-0.38930.00030.65950.1187-0.07881.2006-0.05450.9387-68.807118.7691-24.7655
270.44760.20490.08520.1621-0.04070.1002-0.2337-0.01270.1884-0.0745-0.36370.0673-0.19970.328-0.2790.52630.5318-0.54161.1963-0.41391.1482-78.140219.6968-27.7958
280.0001-0.0183-0.00220.00040.0009-0.0014-0.1046-0.12890.25370.0508-0.29430.6175-0.27870.1614-0.00021.36370.2330.1321.16-0.06460.9145-55.173527.639619.2551
290.0361-0.0114-0.01220.05220.03340.0184-0.5078-0.68040.20980.6478-0.2758-0.0063-0.16880.10370.00011.40350.08680.06690.9983-0.1930.9328-45.37430.178416.4919
300.08960.1312-0.00810.19650.1350.1319-0.29030.0990.11970.35420.00780.5494-1.1689-0.328-0.00030.98590.26570.1221.1536-0.04960.9833-57.375127.85347.3933
310.023-0.00840.02430.005-0.01260.0227-0.1854-0.0868-0.10780.0652-0.211-0.0182-0.31390.2015-01.48090.13770.20070.8849-0.11631.3666-56.232936.597613.1313
32-0.00090.002-0.0051-0.0013-0.0032-0.00250.34060.1616-0.5220.29450.17840.0829-0.1114-0.73340.00060.7398-0.38110.06231.29350.0290.8545-64.0343-3.6150.64
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 65 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 334 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 169 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 170 through 334 )B0
5X-RAY DIFFRACTION5chain 'C' and (resid 3 through 149 )C0
6X-RAY DIFFRACTION6chain 'C' and (resid 150 through 334 )C0
7X-RAY DIFFRACTION7chain 'D' and (resid 3 through 89 )D0
8X-RAY DIFFRACTION8chain 'D' and (resid 90 through 255 )D0
9X-RAY DIFFRACTION9chain 'D' and (resid 256 through 275 )D0
10X-RAY DIFFRACTION10chain 'D' and (resid 276 through 333 )D0
11X-RAY DIFFRACTION11chain 'E' and (resid 2 through 149 )E0
12X-RAY DIFFRACTION12chain 'E' and (resid 150 through 338 )E0
13X-RAY DIFFRACTION13chain 'F' and (resid 3 through 109 )F0
14X-RAY DIFFRACTION14chain 'F' and (resid 110 through 275 )F0
15X-RAY DIFFRACTION15chain 'F' and (resid 276 through 333 )F0
16X-RAY DIFFRACTION16chain 'G' and (resid 0 through 14 )G0
17X-RAY DIFFRACTION17chain 'G' and (resid 15 through 55 )G0
18X-RAY DIFFRACTION18chain 'G' and (resid 56 through 73 )G0
19X-RAY DIFFRACTION19chain 'H' and (resid 3 through 15 )H0
20X-RAY DIFFRACTION20chain 'H' and (resid 16 through 31 )H0
21X-RAY DIFFRACTION21chain 'H' and (resid 32 through 55 )H0
22X-RAY DIFFRACTION22chain 'H' and (resid 56 through 74 )H0
23X-RAY DIFFRACTION23chain 'I' and (resid 6 through 14 )I0
24X-RAY DIFFRACTION24chain 'I' and (resid 15 through 73 )I0
25X-RAY DIFFRACTION25chain 'J' and (resid 0 through 15 )J0
26X-RAY DIFFRACTION26chain 'J' and (resid 16 through 64 )J0
27X-RAY DIFFRACTION27chain 'J' and (resid 65 through 74 )J0
28X-RAY DIFFRACTION28chain 'K' and (resid 3 through 15 )K0
29X-RAY DIFFRACTION29chain 'K' and (resid 16 through 31 )K0
30X-RAY DIFFRACTION30chain 'K' and (resid 32 through 64 )K0
31X-RAY DIFFRACTION31chain 'K' and (resid 65 through 71 )K0
32X-RAY DIFFRACTION32chain 'L' and (resid 35 through 44 )L0

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