[English] 日本語
Yorodumi
- PDB-6rfx: Crystal structure of Eis2 from Mycobacterium abscessus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rfx
TitleCrystal structure of Eis2 from Mycobacterium abscessus
ComponentsEis2
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 ...: / 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
ACETATE ION / CITRIC ACID / polyethylene glycol / Enhanced intracellular survival protein / Uncharacterized N-acetyltransferase D2E36_21790
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Eis2
A: Eis2
B: Eis2
C: Eis2
E: Eis2
F: Eis2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,06824
Polymers272,9816
Non-polymers6,08818
Water29,0761614
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22560 Å2
ΔGint-59 kcal/mol
Surface area88060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.450, 79.800, 152.680
Angle α, β, γ (deg.)90.00, 90.29, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Eis2


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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-P4K / polyethylene glycol / 3,6,9,12,15,18,21,24,27,30,33,36,39,42-tetradecaoxatetratetracontan-1-ol


Mass: 662.804 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C30H62O15
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1614 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: .2 M Ammonium acetate, 0.1 M Sodium citrate pH 5.5, 24% w/v PEG 4000 and 5 mM Hygromycin

-
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: 1.9→50 Å / Num. obs: 212722 / % possible obs: 99.9 % / Redundancy: 6.82 % / Rrim(I) all: 0.13 / Net I/σ(I): 11.09
Reflection shellResolution: 1.9→2 Å / Num. unique obs: 30174 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.15rc3_3435: ???)refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→49.596 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 25.21
RfactorNum. reflection% reflection
Rfree0.226 10537 5 %
Rwork0.2015 --
obs0.2027 210728 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18811 0 190 1614 20615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00219398
X-RAY DIFFRACTIONf_angle_d0.51326344
X-RAY DIFFRACTIONf_dihedral_angle_d13.187051
X-RAY DIFFRACTIONf_chiral_restr0.0632930
X-RAY DIFFRACTIONf_plane_restr0.0033436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.57333000.5125706X-RAY DIFFRACTION86
1.9216-1.94420.41043070.38785843X-RAY DIFFRACTION86
1.9442-1.96790.32753500.31866640X-RAY DIFFRACTION100
1.9679-1.99280.3273530.30226712X-RAY DIFFRACTION100
1.9928-2.0190.30943520.28876678X-RAY DIFFRACTION100
2.019-2.04670.31763560.28866760X-RAY DIFFRACTION100
2.0467-2.07590.33983500.31746674X-RAY DIFFRACTION100
2.0759-2.10690.33513520.28696681X-RAY DIFFRACTION100
2.1069-2.13980.28593520.25346695X-RAY DIFFRACTION100
2.1398-2.17490.27123550.2466731X-RAY DIFFRACTION100
2.1749-2.21240.28463560.24676772X-RAY DIFFRACTION100
2.2124-2.25270.37523500.32476640X-RAY DIFFRACTION99
2.2527-2.2960.28193530.26386705X-RAY DIFFRACTION99
2.296-2.34290.2493530.22136721X-RAY DIFFRACTION100
2.3429-2.39380.2653530.21636695X-RAY DIFFRACTION100
2.3938-2.44950.23433530.21516700X-RAY DIFFRACTION100
2.4495-2.51070.23133560.21276766X-RAY DIFFRACTION100
2.5107-2.57860.24073520.2136697X-RAY DIFFRACTION100
2.5786-2.65450.24733560.22156755X-RAY DIFFRACTION100
2.6545-2.74020.24293540.2146725X-RAY DIFFRACTION100
2.7402-2.83810.25083530.20276717X-RAY DIFFRACTION100
2.8381-2.95170.23023560.20016755X-RAY DIFFRACTION100
2.9517-3.0860.21733540.2046732X-RAY DIFFRACTION100
3.086-3.24870.23413550.21056750X-RAY DIFFRACTION100
3.2487-3.45220.21643580.18476786X-RAY DIFFRACTION100
3.4522-3.71870.17853550.16866749X-RAY DIFFRACTION100
3.7187-4.09270.18493560.15996766X-RAY DIFFRACTION100
4.0927-4.68460.1543600.13616836X-RAY DIFFRACTION100
4.6846-5.90050.16073590.14686830X-RAY DIFFRACTION100
5.9005-49.61260.18163680.1586974X-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)
16.458-1.51240.45179.53742.46472.02650.1469-0.4248-0.71850.4251-0.1078-0.05870.45140.2465-0.02070.22370.013-0.04790.26940.04240.290837.6657-5.56910.9233
24.1277-1.0086-0.19242.6353-0.47733.18420.0097-0.0479-0.10330.1646-0.04060.04660.2110.14130.02990.1509-0.0248-0.00750.1707-0.0340.203331.48341.09847.4158
35.7125-4.0191-7.51782.8855.22869.82490.1885-0.57650.57980.10180.3467-0.4242-0.03540.8784-0.49840.1612-0.0092-0.03650.2353-0.01470.339424.54813.57157.7612
42.1395-0.1589-1.08561.06170.59951.3966-0.10650.0276-0.11270.4739-0.10720.6080.2493-0.34620.21410.3339-0.08340.15610.3027-0.01660.47348.44176.654722.6005
52.0279-0.28950.91792.1762-1.63294.6629-0.2272-0.3379-0.17030.6325-0.02980.35450.14420.09410.26550.5278-0.05850.19370.2465-0.05150.436413.64376.063231.0185
64.69781.081-0.58373.2228-0.82351.069-0.0439-0.06840.01730.5563-0.06220.54150.1461-0.18750.10550.2847-0.05660.13720.2443-0.08760.370110.166917.100226.3098
70.821-0.0506-0.54961.4901-0.22981.5252-0.03940.13090.1108-0.1789-0.03560.333-0.0293-0.23560.07560.1425-0.012-0.06820.2702-0.03420.357517.50119.6684-5.094
85.19921.21541.51268.3512-4.65057.51380.2572-0.42120.63240.7092-0.07120.1164-0.6293-0.2141-0.18740.29280.01390.01970.2805-0.10520.39617.042357.877934.5217
90.90010.0197-1.09270.83220.5824.03540.0522-0.03610.14650.0986-0.07410.0927-0.149-0.24820.0290.18350.0344-0.05080.2141-0.02860.47135.593451.273527.6581
109.0984-8.0037-2.95777.47232.91841.1795-0.4662-0.5525-0.22510.43580.1170.49120.1816-0.01680.34490.1851-0.0193-0.04190.303-0.01420.47566.950239.897120.4355
110.6717-1.1367-0.3933.99450.60041.13790.04170.24150.1764-0.2069-0.0868-0.1875-0.17190.06240.03950.1357-0.05-0.01640.26210.0420.324426.659345.72559.989
122.04420.9405-0.14583.18921.87825.07540.0593-0.0949-0.02050.20880.0315-0.15130.05390.297-0.07690.1041-0.0109-0.02610.2230.0290.358331.972341.039214.5722
131.43970.42480.1850.45280.16650.56860.01480.1945-0.1568-0.006-0.21560.5019-0.0319-0.2730.170.15710.031-0.04410.4524-0.15740.69610.296632.655710.4872
146.0717-1.3981-3.00286.5508-2.58983.2214-0.36130.07860.5548-0.03180.18670.1469-0.4781-0.19660.21180.309-0.0472-0.15260.34870.01530.316951.085457.506316.8083
152.3329-1.75910.45662.3492-0.6672.6856-0.14340.26580.1070.0825-0.0005-0.0098-0.36430.09570.13990.2214-0.1096-0.04530.26330.01880.235757.644350.778618.9181
161.5760.1551-0.12172.0499-3.10696.7264-0.11810.47450.2182-0.33550.44070.55280.5344-0.8391-0.23620.2561-0.1126-0.07120.37110.03010.302961.567639.038123.4294
170.8227-0.00910.39361.4331-0.31783.2867-0.083-0.17550.080.73770.0249-0.1815-0.39010.27860.06780.4975-0.01-0.09370.2847-0.04450.244362.752145.047145.9648
187.9086-0.88710.93113.51020.68225.0981-0.1483-0.2418-0.00250.70560.09690.139-0.1951-0.17330.05470.50370.01990.01720.178-0.01680.180855.520242.315149.3356
191.05320.24780.02511.5651-0.44961.4638-0.07630.13460.05410.1219-0.0087-0.36610.00240.66090.06970.1915-0.0305-0.07980.47430.00610.288173.476131.743924.3052
204.4291-1.7842.06081.68-1.39721.28970.0817-0.1173-0.4360.13060.06120.14780.7006-0.1215-0.16411.06670.1076-0.01560.32430.01570.295555.33-6.147954.7545
212.11460.3376-0.55271.1085-0.54971.466-0.1051-0.2799-0.05610.31540.07210.02330.52070.15220.02860.81490.1449-0.06660.2832-0.02030.260861.30030.488750.9935
221.5077-0.85573.04761.6412-3.25058.1239-0.3712-0.49290.09310.94240.2679-0.0507-0.2557-0.28250.11440.58010.108-0.1140.3271-0.01830.278865.450911.969245.1402
231.1804-0.0299-0.33313.0537-0.29861.45490.03510.1317-0.1238-0.13220.0258-0.03080.49790.1897-0.05850.37540.0362-0.07470.2883-0.05280.159759.49696.244923.735
245.35742.0284-0.9434.6585-0.42643.9544-0.01060.11810.05830.12750.01520.29540.334-0.1428-0.00330.25610.0222-0.06470.2031-0.01720.137752.612610.799423.1227
252.72080.0111.37320.9987-0.23852.20180.0113-0.120.01990.4938-0.0425-0.39690.17570.57410.03870.47460.0854-0.19110.4575-0.02340.312877.310519.244943.3944
269.8165-1.27324.23252.2464-2.40125.1534-0.15940.38420.81120.1385-0.1867-0.0976-0.09590.28540.34630.3928-0.05230.03980.2087-0.02220.315640.355256.06462.9296
278.63760.9171-1.08691.77970.11622.6086-0.10950.01630.27780.2655-0.12020.08970.30670.16960.21110.538-0.00560.03720.2609-0.03650.186839.260448.27569.2213
288.98950.73991.98421.6101-1.28021.77080.1810.2585-0.08450.2909-0.23840.05280.312-0.0590.05650.6936-0.0730.04330.3606-0.09070.238139.058544.193174.3886
291.68841.11280.63362.49790.80021.56120.0246-0.24040.55910.3538-0.24570.9199-0.0061-0.29590.2170.3626-0.0310.12440.3157-0.11370.540814.704643.592259.6239
303.1456-0.32040.78314.5059-2.06314.8549-0.1125-0.06310.52310.0678-0.11320.5740.0595-0.13340.21910.2872-0.04070.03450.2348-0.13350.465214.259440.856452.304
310.29230.12120.26190.22020.02750.42930.2527-0.30940.140.6935-0.35250.29470.413-0.20940.07121.0378-0.26310.16460.5187-0.12420.252727.322131.541881.0875
321.5519-0.82480.02670.6205-0.38922.07280.38310.2117-0.43770.4972-0.35360.41930.4284-0.20370.01691.0485-0.34010.23430.4003-0.04490.471110.1898-1.63352.532
331.0426-0.16660.84440.1666-0.06380.6942-0.20920.14940.02030.0289-0.36790.08780.1610.03840.45041.248-0.59320.52560.6947-0.06890.66064.41326.737559.5842
340.29360.1459-0.2122.27-0.46240.35050.129-0.2489-0.14820.664-0.0997-0.10180.7211-0.0677-0.01851.0935-0.1325-0.00160.35230.01840.308431.93027.56166.4715
353.4374-0.6878-0.76622.6196-0.37491.09510.16210.0514-0.10830.25170.0061-0.12880.6033-0.0977-0.17070.854-0.0429-0.04280.24920.00910.267137.395910.476761.7036
360.64210.2603-0.14550.2945-0.06810.1010.275-0.39320.13130.8358-0.34140.22250.4631-0.37940.02931.1094-0.46160.47860.7544-0.14810.41378.295317.027671.575
371.0762-0.42890.54071.15140.1920.49270.0037-0.6370.20030.5662-0.20470.35930.394-0.47950.09811.1518-0.50210.57360.7697-0.21310.38417.196121.224774.0223
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 3 through 25 )
2X-RAY DIFFRACTION2chain 'D' and (resid 26 through 109 )
3X-RAY DIFFRACTION3chain 'D' and (resid 110 through 139 )
4X-RAY DIFFRACTION4chain 'D' and (resid 140 through 199 )
5X-RAY DIFFRACTION5chain 'D' and (resid 200 through 242 )
6X-RAY DIFFRACTION6chain 'D' and (resid 243 through 298 )
7X-RAY DIFFRACTION7chain 'D' and (resid 299 through 411 )
8X-RAY DIFFRACTION8chain 'A' and (resid 3 through 25 )
9X-RAY DIFFRACTION9chain 'A' and (resid 26 through 108 )
10X-RAY DIFFRACTION10chain 'A' and (resid 109 through 139 )
11X-RAY DIFFRACTION11chain 'A' and (resid 140 through 199 )
12X-RAY DIFFRACTION12chain 'A' and (resid 200 through 285 )
13X-RAY DIFFRACTION13chain 'A' and (resid 286 through 411 )
14X-RAY DIFFRACTION14chain 'B' and (resid 3 through 25 )
15X-RAY DIFFRACTION15chain 'B' and (resid 26 through 108 )
16X-RAY DIFFRACTION16chain 'B' and (resid 109 through 139 )
17X-RAY DIFFRACTION17chain 'B' and (resid 140 through 199 )
18X-RAY DIFFRACTION18chain 'B' and (resid 200 through 273 )
19X-RAY DIFFRACTION19chain 'B' and (resid 274 through 411 )
20X-RAY DIFFRACTION20chain 'C' and (resid 3 through 25 )
21X-RAY DIFFRACTION21chain 'C' and (resid 26 through 108 )
22X-RAY DIFFRACTION22chain 'C' and (resid 109 through 139 )
23X-RAY DIFFRACTION23chain 'C' and (resid 140 through 199 )
24X-RAY DIFFRACTION24chain 'C' and (resid 200 through 285 )
25X-RAY DIFFRACTION25chain 'C' and (resid 286 through 411 )
26X-RAY DIFFRACTION26chain 'E' and (resid 3 through 51 )
27X-RAY DIFFRACTION27chain 'E' and (resid 52 through 93 )
28X-RAY DIFFRACTION28chain 'E' and (resid 94 through 129 )
29X-RAY DIFFRACTION29chain 'E' and (resid 130 through 199 )
30X-RAY DIFFRACTION30chain 'E' and (resid 200 through 285 )
31X-RAY DIFFRACTION31chain 'E' and (resid 286 through 411 )
32X-RAY DIFFRACTION32chain 'F' and (resid 3 through 93 )
33X-RAY DIFFRACTION33chain 'F' and (resid 94 through 129 )
34X-RAY DIFFRACTION34chain 'F' and (resid 130 through 199 )
35X-RAY DIFFRACTION35chain 'F' and (resid 200 through 285 )
36X-RAY DIFFRACTION36chain 'F' and (resid 286 through 342 )
37X-RAY DIFFRACTION37chain 'F' and (resid 343 through 411 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more