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- PDB-6rft: Crystal structure of Eis2 from Mycobacterium abscessus bound to A... -

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Basic information

Entry
Database: PDB / ID: 6rft
TitleCrystal structure of Eis2 from Mycobacterium abscessus bound to Acetyl-CoA
ComponentsUncharacterized N-acetyltransferase D2E36_21790
KeywordsANTIBIOTIC / GCN5 N-acetyltransferase / Eis
Function / homology
Function and homology information


aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
N-acetyltransferase Eis / Enhanced intracellular survival protein domain / Eis-like, acetyltransferase domain / Sterol carrier protein domain / Acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) domain / SCP2 sterol-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase ...N-acetyltransferase Eis / Enhanced intracellular survival protein domain / Eis-like, acetyltransferase domain / Sterol carrier protein domain / Acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) domain / SCP2 sterol-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / Enhanced intracellular survival protein / Uncharacterized N-acetyltransferase D2E36_21790
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBlaise, M. / Kremer, L. / Olieric, V. / Alsarraf, H. / Ung, K.L.
CitationJournal: Febs J. / Year: 2019
Title: Crystal structure of the aminoglycosides N-acetyltransferase Eis2 from Mycobacterium abscessus.
Authors: Ung, K.L. / Alsarraf, H.M.A.B. / Olieric, V. / Kremer, L. / Blaise, M.
History
DepositionApr 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized N-acetyltransferase D2E36_21790
B: Uncharacterized N-acetyltransferase D2E36_21790
C: Uncharacterized N-acetyltransferase D2E36_21790
D: Uncharacterized N-acetyltransferase D2E36_21790
E: Uncharacterized N-acetyltransferase D2E36_21790
F: Uncharacterized N-acetyltransferase D2E36_21790
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,83812
Polymers272,9816
Non-polymers4,8576
Water17,439968
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27960 Å2
ΔGint-83 kcal/mol
Surface area85580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.650, 76.990, 152.560
Angle α, β, γ (deg.)90.00, 90.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized N-acetyltransferase D2E36_21790


Mass: 45496.797 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: D2E36_21790 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A3A1BNP8, UniProt: A0A1M9A4M7*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 968 / 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: 48.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M BIS-TRIS pH 5.5, 27% PEG 3350 and 2 mM acetyl-CoA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.973 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.3→48.939 Å / Num. obs: 115359 / % possible obs: 100 % / Redundancy: 6.81 % / Rrim(I) all: 0.224 / Net I/σ(I): 8.35
Reflection shellResolution: 2.3→2.4 Å / Num. unique obs: 13735 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.15rc3_3435: ???)refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.939 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.4
RfactorNum. reflection% reflection
Rfree0.2666 1996 1.73 %
Rwork0.229 --
obs0.2297 115356 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→48.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18824 0 285 968 20077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00219520
X-RAY DIFFRACTIONf_angle_d0.50626592
X-RAY DIFFRACTIONf_dihedral_angle_d9.61411523
X-RAY DIFFRACTIONf_chiral_restr0.0422972
X-RAY DIFFRACTIONf_plane_restr0.0033431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.34551420.29638041X-RAY DIFFRACTION100
2.3575-2.42120.34351460.30548061X-RAY DIFFRACTION100
2.4212-2.49250.38021410.3098020X-RAY DIFFRACTION100
2.4925-2.57290.38841410.30348075X-RAY DIFFRACTION100
2.5729-2.66490.36831480.28938058X-RAY DIFFRACTION100
2.6649-2.77160.34311360.27858064X-RAY DIFFRACTION100
2.7716-2.89770.31331400.26978025X-RAY DIFFRACTION100
2.8977-3.05050.27251450.25128089X-RAY DIFFRACTION100
3.0505-3.24150.30681420.25018081X-RAY DIFFRACTION100
3.2415-3.49180.22921400.22528128X-RAY DIFFRACTION100
3.4918-3.8430.25021420.21098076X-RAY DIFFRACTION100
3.843-4.39880.2331450.18488114X-RAY DIFFRACTION100
4.3988-5.54080.21851420.17338195X-RAY DIFFRACTION100
5.5408-48.94970.1811460.18848333X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.02191.02911.57641.82540.791.1067-0.14630.008-0.25990.01840.00380.07730.0724-0.09570.11520.2340.01880.07330.2340.01050.243221.5895-1.960469.2457
20.95370.3003-0.67230.8520.27731.3381-0.02750.1146-0.0241-0.23750.00790.0347-0.13890.0070.0180.280.0009-0.01290.17580.03160.193141.70628.80654.801
39.08070.7232-2.992.1381-0.16123.80620.17490.0239-0.17720.45130.0535-0.31390.0367-0.1597-0.19040.47450.0224-0.12180.1861-0.02370.20540.774716.629784.8266
42.30750.0497-0.32111.9815-0.03440.06270.0387-0.3472-0.0350.27270.0123-0.09170.128-0.0076-0.04510.37160.0082-0.06040.24690.00540.152936.768120.092981.6768
54.95362.9923-1.30372.4609-0.47520.48760.08460.16780.51880.04250.13340.24950.30140.0313-0.1940.804-0.0275-0.16850.35320.03870.366212.018553.922311.0127
61.18840.0417-0.09441.3953-0.41410.3378-0.14090.08580.43560.17950.0989-0.0257-0.2135-0.16360.05340.9413-0.0454-0.17470.3260.09910.305720.117148.96028.7299
71.4693-1.24080.50920.8181-0.2341-0.00860.18350.01560.0606-0.2282-0.1940.1196-0.04730.01380.0130.9571-0.0679-0.18580.4140.00710.349518.250737.3196.9196
82.63-0.97070.30232.8180.29030.6568-0.11660.04240.1733-0.08360.1249-0.044-0.08520.0173-0.00030.5692-0.0489-0.07070.21450.01980.200341.946640.774520.2052
91.3062-0.55230.8490.4055-0.7151.07020.09450.1772-0.20490.0526-0.16520.17420.2055-0.1818-0.07331.18620.0875-0.17840.07310.2605-0.123934.299527.651212.7356
102.6503-0.37260.67071.3142-0.68461.98790.02130.4731-0.0504-0.1124-0.0919-0.13870.07910.20580.03251.0039-0.0292-0.06330.41710.05560.218731.034129.7266-11.3757
110.6925-0.51280.05770.56090.19330.3704-0.00920.52010.2409-0.6608-0.0802-0.1179-0.07350.00760.11551.2329-0.1012-0.16950.51660.06780.35125.535829.5801-15.1659
120.3661-0.29060.11240.5896-0.91571.7224-0.0388-0.16320.1150.014-0.086-0.421-0.16510.39790.07521.3017-0.0955-0.33710.31220.0543-0.300825.847124.248-2.8284
132.6567-0.3253-0.53062.3099-1.18210.7976-0.16880.1685-0.2152-0.12910.1531-0.30940.29390.05710.03880.74540.0365-0.04020.35240.05580.185631.067424.5324-2.6771
141.34310.19850.11172.0092-1.12993.63480.0550.17140.1175-0.257-0.0014-0.0323-0.35420.1853-0.06120.3344-0.04010.02380.2027-0.02570.264947.194752.284346.8908
153.5046-1.0035-1.26232.6483-0.52845.65310.09690.0781-0.0480.0206-0.2755-0.38380.0265-0.02570.13140.2869-0.0379-0.04460.1819-0.02990.278655.000143.919847.4798
167.62333.4316-1.71291.6865-0.69830.3204-0.17990.513-0.05170.04560.2347-0.09070.0709-0.1209-0.05920.45190.036-0.08470.2806-0.030.203240.035231.92754.446
172.23350.0838-0.33262.7562-0.83451.06680.10350.06140.1633-0.2821-0.02290.16620.10350.0257-0.09810.2456-0.04710.01140.1961-0.03220.172426.951645.099563.2075
181.63050.17230.90183.38371.85755.6494-0.08370.00260.0854-0.1133-0.06580.1655-0.30190.03750.12020.1651-0.03320.07620.19610.02140.21523.178235.82464.3939
195.69174.0596-2.50173.3848-1.45931.6887-0.3058-0.04850.1576-0.37890.12410.1758-0.04340.14540.20290.315-0.0182-0.06650.1607-0.00480.206536.880629.917661.5876
206.8062-0.0081-5.49952.4392-0.89046.1038-0.06060.05650.24350.09890.03580.0774-0.07290.32010.02130.1635-0.0421-0.08710.2236-0.01080.177658.848433.845770.8826
211.8999-0.32381.31213.26480.41571.5220.0364-0.02520.02530.5003-0.1052-0.66380.21840.40770.02850.2314-0.0377-0.04880.2647-0.01280.286764.915333.64768.3693
221.8093-0.35150.14262.5775-0.01720.9221-0.1049-0.0339-0.06880.10230.0707-0.1265-0.1186-0.01780.03310.1898-0.0121-0.00930.2007-0.04410.160752.955827.769764.829
236.9185-2.2268-3.22386.0970.64924.37520.2014-0.05-0.5711-0.280.12510.21060.36180.1763-0.26630.5912-0.0305-0.09960.24510.00280.214447.7165-8.950229.9637
241.01980.2708-0.25161.415-1.96842.69120.0981-0.0087-0.152-0.1243-0.0965-0.07490.02310.17910.00280.61370.0204-0.06470.2021-0.0540.33647.25-2.4122.8334
254.58091.82330.91532.1565-0.97641.40350.1392-0.39720.49170.0292-0.34010.4251-0.1668-0.21980.14670.80520.0561-0.02450.38-0.08390.277948.6027.114417.4064
263.7395-0.1228-1.02190.7051-0.09590.89510.25330.05860.06-0.05770.04580.15740.0632-0.0855-0.20820.85120.0134-0.2180.2346-0.02790.27419.954515.967710.6097
273.5302-0.0955-0.5691.576-0.97680.70320.0245-0.0177-0.06190.03480.01810.0727-0.1270.0451-0.02340.7021-0.0592-0.14280.22550.00340.263322.9539-1.435213.4907
283.52460.2045-0.8821.48010.0731.69270.1488-0.1794-0.0268-0.1093-0.03420.15960.4001-0.1622-0.14410.6059-0.0126-0.11740.2686-0.00440.253618.47449.676313.3114
291.8030.0077-0.12760.5696-0.29650.2124-0.14870.1859-0.049-0.22240.0204-0.15450.15290.01940.13290.80620.0216-0.02530.2771-0.05650.279447.533113.87583.6419
301.67191.14790.60481.41130.52810.265-0.21160.1730.0976-0.40890.17780.0099-0.0714-0.00140.01740.86010.0249-0.06830.3547-0.02750.278847.016218.55965.588
311.8883-2.0457-1.78485.53942.08651.67560.13150.03210.1892-0.61470.2267-0.3449-1.03740.2103-0.25541.2934-0.1031-0.19310.2225-0.04480.42584.664355.385658.9645
321.7064-1.1169-0.52223.63010.01482.48530.08830.31270.04-0.44870.123-0.0746-1.09130.1794-0.241.0413-0.0163-0.05690.3267-0.03320.33973.411153.168254.1196
330.88580.16851.06140.62340.2183.16120.10030.10550.1815-0.0455-0.2175-0.0143-0.4248-0.67420.05460.8330.3362-0.13320.4789-0.02290.1472-14.039845.149147.9844
348.97423.92572.13951.77450.59384.13970.3841-0.2321-0.03430.0724-0.4429-0.1272-0.2983-0.16310.00870.49130.13860.00760.2139-0.01410.2684-4.048544.009461.2957
351.0618-1.0429-2.00572.26634.0497.38150.0614-0.0449-0.0448-0.11330.16760.0153-0.44980.2263-0.22490.56260.0748-0.03690.2128-0.00590.2945-2.116131.156845.5559
360.52120.502-0.01341.12620.01750.9294-0.1240.0653-0.0821-0.2880.1785-0.1152-0.9345-0.1234-0.00661.26950.21-0.15470.37210.0240.1856-3.840343.588128.7207
374.91510.54360.24481.95610.48231.0304-0.11670.18620.2984-0.36980.0315-0.0825-0.4192-0.02630.07550.70770.1053-0.00670.276-0.02520.2129-2.026634.880226.766
380.8233-0.4123-0.75881.97480.77573.1890.1056-0.03320.0381-0.1799-0.20030.4388-0.3488-0.62480.09190.32620.0937-0.0560.3836-0.0680.2968-18.630229.516551.8348
393.0997-0.3763-1.38740.98390.67233.776-0.0409-0.0516-0.0680.06910.0247-0.06670.9905-0.0183-0.00970.918-0.0434-0.160.3236-0.01460.29-4.9415-3.253525.2893
400.56770.0040.30512.27110.79841.91360.0491-0.0437-0.06430.15110.0177-0.1480.5885-0.1424-0.06170.6418-0.0497-0.09350.235-0.00560.2544-1.06816.844650.7464
411.7285-0.02520.59311.98821.45542.69490.25980.1404-0.0012-0.079-0.4470.29230.1295-0.82530.19910.49540.0016-0.03950.4852-0.06080.2406-20.916516.663733.223
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 306 )
3X-RAY DIFFRACTION3chain 'A' and (resid 307 through 327 )
4X-RAY DIFFRACTION4chain 'A' and (resid 328 through 411 )
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 25 )
6X-RAY DIFFRACTION6chain 'B' and (resid 26 through 81 )
7X-RAY DIFFRACTION7chain 'B' and (resid 82 through 144 )
8X-RAY DIFFRACTION8chain 'B' and (resid 145 through 280 )
9X-RAY DIFFRACTION9chain 'B' and (resid 281 through 306 )
10X-RAY DIFFRACTION10chain 'B' and (resid 307 through 327 )
11X-RAY DIFFRACTION11chain 'B' and (resid 328 through 357 )
12X-RAY DIFFRACTION12chain 'B' and (resid 358 through 380 )
13X-RAY DIFFRACTION13chain 'B' and (resid 381 through 411 )
14X-RAY DIFFRACTION14chain 'C' and (resid 2 through 81 )
15X-RAY DIFFRACTION15chain 'C' and (resid 82 through 120 )
16X-RAY DIFFRACTION16chain 'C' and (resid 121 through 144 )
17X-RAY DIFFRACTION17chain 'C' and (resid 145 through 249 )
18X-RAY DIFFRACTION18chain 'C' and (resid 250 through 280 )
19X-RAY DIFFRACTION19chain 'C' and (resid 281 through 306 )
20X-RAY DIFFRACTION20chain 'C' and (resid 307 through 327 )
21X-RAY DIFFRACTION21chain 'C' and (resid 328 through 357 )
22X-RAY DIFFRACTION22chain 'C' and (resid 358 through 411 )
23X-RAY DIFFRACTION23chain 'D' and (resid 3 through 25 )
24X-RAY DIFFRACTION24chain 'D' and (resid 26 through 108 )
25X-RAY DIFFRACTION25chain 'D' and (resid 109 through 129 )
26X-RAY DIFFRACTION26chain 'D' and (resid 130 through 156 )
27X-RAY DIFFRACTION27chain 'D' and (resid 157 through 239 )
28X-RAY DIFFRACTION28chain 'D' and (resid 240 through 280 )
29X-RAY DIFFRACTION29chain 'D' and (resid 281 through 357 )
30X-RAY DIFFRACTION30chain 'D' and (resid 358 through 411 )
31X-RAY DIFFRACTION31chain 'E' and (resid 2 through 25 )
32X-RAY DIFFRACTION32chain 'E' and (resid 26 through 60 )
33X-RAY DIFFRACTION33chain 'E' and (resid 61 through 81 )
34X-RAY DIFFRACTION34chain 'E' and (resid 82 through 120 )
35X-RAY DIFFRACTION35chain 'E' and (resid 121 through 144 )
36X-RAY DIFFRACTION36chain 'E' and (resid 145 through 239 )
37X-RAY DIFFRACTION37chain 'E' and (resid 240 through 280 )
38X-RAY DIFFRACTION38chain 'E' and (resid 281 through 411 )
39X-RAY DIFFRACTION39chain 'F' and (resid 3 through 120 )
40X-RAY DIFFRACTION40chain 'F' and (resid 121 through 280 )
41X-RAY DIFFRACTION41chain 'F' and (resid 281 through 411 )

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