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- PDB-6mmz: Crystal structure of meta-AAC0038, an environmental aminoglycosid... -

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Basic information

Entry
Database: PDB / ID: 6mmz
TitleCrystal structure of meta-AAC0038, an environmental aminoglycoside resistance enzyme, H29A mutant apoenzyme
ComponentsAminoglycoside N(3)-acetyltransferase
KeywordsTRANSFERASE / ANTIBIOTIC_NAT FAMILY / ACETYLTRANSFERASE / AMINOGLYCOSIDE / ANTIBIOTIC RESISTANCE / METAGENOME / SOIL / COENZYME A / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / National Institute of Allergy and Infectious Diseases / NIAID
Function / homologyaminoglycoside 3-N-acetyltransferase / aminoglycoside 3-N-acetyltransferase activity / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like / response to antibiotic / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsStogios, P.J. / Skarina, T. / Xu, Z. / Yim, V. / Savchenko, A. / Joachimiak, A. / Satchell, K.J. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Commun Biol / Year: 2022
Title: Structural and molecular rationale for the diversification of resistance mediated by the Antibiotic_NAT family.
Authors: Stogios, P.J. / Bordeleau, E. / Xu, Z. / Skarina, T. / Evdokimova, E. / Chou, S. / Diorio-Toth, L. / D'Souza, A.W. / Patel, S. / Dantas, G. / Wright, G.D. / Savchenko, A.
History
DepositionOct 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 26, 2020Group: Database references / Category: pdbx_database_related
Revision 1.3Apr 6, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminoglycoside N(3)-acetyltransferase
B: Aminoglycoside N(3)-acetyltransferase
C: Aminoglycoside N(3)-acetyltransferase
D: Aminoglycoside N(3)-acetyltransferase
E: Aminoglycoside N(3)-acetyltransferase
F: Aminoglycoside N(3)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,39630
Polymers173,3336
Non-polymers2,06324
Water1,874104
1
A: Aminoglycoside N(3)-acetyltransferase
B: Aminoglycoside N(3)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3548
Polymers57,7782
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Aminoglycoside N(3)-acetyltransferase
D: Aminoglycoside N(3)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,52111
Polymers57,7782
Non-polymers7439
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Aminoglycoside N(3)-acetyltransferase
F: Aminoglycoside N(3)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,52111
Polymers57,7782
Non-polymers7439
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.761, 158.124, 143.440
Angle α, β, γ (deg.)90.00, 94.87, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-303-

SO4

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Components

#1: Protein
Aminoglycoside N(3)-acetyltransferase


Mass: 28888.826 Da / Num. of mol.: 6 / Mutation: H29A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic
References: UniProt: A0A059X981, aminoglycoside 3-N-acetyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.48 Å3/Da / Density % sol: 64.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2.5 M ammonium sulfate, 0.1 M bis-tris propane pH 7, 10 mM gentamicin

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→19.75 Å / Num. obs: 35143 / % possible obs: 99.4 % / Redundancy: 4.6 % / CC1/2: 0.964 / Rmerge(I) obs: 0.268 / Rpim(I) all: 0.142 / Net I/σ(I): 6.3
Reflection shellResolution: 3.3→3.46 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4652 / CC1/2: 0.809 / Rpim(I) all: 0.395 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(dev_3092: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HT0

5ht0


Resolution: 3.3→19.75 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.14
RfactorNum. reflection% reflectionSelection details
Rfree0.2605 1646 4.69 %RANDOM
Rwork0.2037 ---
obs0.2064 35122 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11977 0 104 104 12185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212345
X-RAY DIFFRACTIONf_angle_d0.55216789
X-RAY DIFFRACTIONf_dihedral_angle_d15.4184477
X-RAY DIFFRACTIONf_chiral_restr0.0431798
X-RAY DIFFRACTIONf_plane_restr0.0032204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.39660.38861470.29562758X-RAY DIFFRACTION100
3.3966-3.50570.34091310.27042790X-RAY DIFFRACTION100
3.5057-3.63020.31281330.24632771X-RAY DIFFRACTION100
3.6302-3.77460.28481310.22532800X-RAY DIFFRACTION100
3.7746-3.94510.31511280.22262804X-RAY DIFFRACTION100
3.9451-4.15130.26431210.20492769X-RAY DIFFRACTION100
4.1513-4.40870.24681580.18872781X-RAY DIFFRACTION100
4.4087-4.74470.22321530.17312787X-RAY DIFFRACTION100
4.7447-5.21420.21491310.16462771X-RAY DIFFRACTION100
5.2142-5.95060.23461250.18222826X-RAY DIFFRACTION100
5.9506-7.43020.21971600.19042776X-RAY DIFFRACTION100
7.4302-19.75150.21441280.17362843X-RAY DIFFRACTION99
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)
11.87390.6544-1.20611.64640.32691.79120.1847-0.1917-0.06310.3798-0.1594-0.25590.4610.8157-0.02560.24960.1831-0.05850.6794-0.01660.4419116.2275-15.7985300.6189
25.9622-5.6578-1.13845.51031.80734.2805-0.5885-1.0393-0.48990.39810.93541.1581.0346-0.0197-0.29140.34770.04980.07540.41670.09770.847385.3907-3.381300.5627
31.4439-0.18430.49712.4029-0.34711.35360.1432-0.2333-0.1466-0.0370.0790.21120.48160.3269-0.23050.37360.1363-0.02240.307-0.02930.336698.362-21.9467299.7235
45.013-0.24020.38073.12620.21412.40310.1785-0.4287-0.1428-0.09110.11210.256-0.48480.4037-0.26010.2485-0.04750.00970.2922-0.02850.296897.320211.9904299.1439
53.7528-2.8606-3.55394.36822.48914.1729-0.4006-1.61851.19561.33041.0868-1.14770.03570.29-0.66560.59460.0431-0.01790.8684-0.28850.8213127.8607-0.5614304.3529
62.68870.37230.78722.26131.0070.59990.2896-0.18240.3357-0.43060.1588-0.1098-0.41180.6763-0.35750.3647-0.18190.03190.502-0.16980.41113.76169.776294.9057
71.4038-0.8112-0.54091.32390.34081.06030.0036-0.65850.53610.06330.3994-0.5469-0.27870.9484-0.25740.3626-0.29280.07960.7413-0.24990.5393115.826421.922304.1092
84.9995-0.9460.98727.4476-3.49215.2261-0.2473-0.20120.5440.4816-0.098-0.7303-0.41770.58110.28520.4611-0.0735-0.03840.455-0.02320.284120.444950.8338326.3038
91.25891.5565-1.21273.8415-0.36344.5824-0.0218-0.33110.04170.1485-0.03360.43770.3528-0.363-0.00360.4638-0.1147-0.14830.4583-0.04670.2182108.498939.3489326.9653
102.8745-1.85523.07567.9221-3.06013.45930.6062-1.5754-0.4293-0.38770.24651.1554-0.267-0.2604-0.76550.6324-0.2759-0.05230.7650.15320.452988.954734.5018324.2117
112.72740.38821.46750.98570.62883.79820.0804-0.2066-0.20780.3787-0.0873-0.15960.1665-0.2413-0.00730.5469-0.1233-0.01530.35080.03760.3365110.293336.6067328.9726
125.7529-1.0385-3.96093.4373-2.45245.8201-0.1642-0.2661-0.66621.2858-0.04570.3950.9892-0.54940.17181.3811-0.2525-0.04280.5563-0.0790.354106.594330.2352345.6128
134.38350.53090.66413.1207-1.07254.44290.2354-0.1041-0.66270.62450.11980.37830.8854-0.3302-0.21150.5557-0.40690.09950.5563-0.0390.489494.208626.545329.2792
143.3596-0.14660.43432.9671-0.60671.75880.2101-0.4558-0.04240.5179-0.4095-0.40790.8255-0.37630.23231.1822-0.12640.02270.72520.0590.3626108.642140.6698347.6952
154.30224.4686-1.04797.106-2.52239.78560.0682-0.3260.71861.5351-0.6131-0.4951-0.99091.2230.42290.5001-0.1559-0.08580.5211-0.1130.495121.703149.2663338.5644
162.2883-0.4995-4.22573.68970.21127.93930.2576-0.9507-0.29970.6791-0.073-0.10781.01670.0105-0.04031.115-0.1818-0.11810.9280.01490.2811113.067732.9795351.5019
173.7853-0.5582-0.80643.5714-0.77345.3144-0.0809-0.1625-0.07780.02270.45620.22780.4829-0.6836-0.22780.3585-0.188-0.02040.53150.04730.406290.927847.4377310.1973
188.97763.57825.4692.53313.0714.13460.2294-0.04961.18340.8716-0.85060.0359-0.0928-0.07580.58690.6089-0.29310.06430.4488-0.03920.588119.275759.8269312.0788
192.32690.5555-1.12291.7483-2.7094.18880.13970.0217-0.01740.05320.02260.36460.4211-0.4058-0.13630.3595-0.1864-0.02220.3401-0.01890.334104.300251.1951303.8524
200.87910.1801-0.05011.8609-0.95072.0985-0.01630.14110.24-0.02470.27340.2769-0.0274-0.7439-0.22020.2514-0.064-0.02230.52110.0690.37697.078763.0361298.7104
213.90961.4111-0.8285.7434-3.41044.0178-0.15070.0882-0.4751-0.64580.3178-0.459-0.29480.8223-0.12290.6406-0.27460.1140.7376-0.090.3388127.274224.3962248.0161
220.4772-0.1398-0.90294.74890.11361.71460.0438-0.0084-0.0855-0.4031-0.1050.4562-0.1835-0.21040.23470.767-0.57070.13950.6081-0.08670.5207115.329736.1659245.2078
234.2241-0.36490.13444.2677-0.33470.3164-0.62851.2906-0.481-0.54850.45310.8938-0.37270.2710.24691.0332-0.497-0.11330.5664-0.05120.611695.940340.3371244.65
242.4228-0.6237-0.08282.6329-0.86110.9480.09680.3653-0.015-0.42650.1071-0.015-0.24920.0245-0.14030.8698-0.57730.03930.4633-0.02790.4051114.906939.8342246.0881
251.4211-0.6863-0.25671.6828-0.72890.55610.07390.35620.2024-0.34950.08950.1385-0.10290.0086-0.17150.9491-0.40320.02740.76140.01990.4421113.199443.3916235.7973
260.9611-0.48860.24011.3-0.29532.599-0.2228-0.01990.0415-0.54340.502-0.456-0.2063-0.1824-0.21011.1843-0.38880.12260.8043-0.04620.381123.863135.2476226.5715
273.97370.67430.33971.60920.3432.2937-0.08030.53510.1150.00460.17460.1636-1.11280.4167-0.00050.7248-0.19270.01450.32570.01680.388593.867128.7351259.0006
285.36942.83280.94881.7405-0.43223.6141.1342-0.3744-1.5815-0.4633-0.20360.36110.32850.5625-0.67740.6735-0.2095-0.2750.5519-0.05960.8036123.42113.3566261.0337
292.3392-0.00170.94833.7444-0.76113.04020.24540.0948-0.0981-0.2938-0.005-0.0837-0.43690.6267-0.17470.6775-0.36120.02380.3484-0.06660.374107.742626.1236264.1421
301.78780.7341-0.35281.20170.1471.7631-0.017-0.0385-0.0866-0.13070.0717-0.1722-0.39540.2306-0.03180.3132-0.10630.00650.2399-0.01710.2851100.89212.8636271.7849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 65 )
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 262 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 65 )
5X-RAY DIFFRACTION5chain 'B' and (resid 66 through 85 )
6X-RAY DIFFRACTION6chain 'B' and (resid 86 through 142 )
7X-RAY DIFFRACTION7chain 'B' and (resid 143 through 262 )
8X-RAY DIFFRACTION8chain 'C' and (resid 4 through 51 )
9X-RAY DIFFRACTION9chain 'C' and (resid 52 through 69 )
10X-RAY DIFFRACTION10chain 'C' and (resid 70 through 88 )
11X-RAY DIFFRACTION11chain 'C' and (resid 89 through 165 )
12X-RAY DIFFRACTION12chain 'C' and (resid 166 through 180 )
13X-RAY DIFFRACTION13chain 'C' and (resid 181 through 202 )
14X-RAY DIFFRACTION14chain 'C' and (resid 203 through 226 )
15X-RAY DIFFRACTION15chain 'C' and (resid 227 through 243 )
16X-RAY DIFFRACTION16chain 'C' and (resid 244 through 263 )
17X-RAY DIFFRACTION17chain 'D' and (resid 3 through 69 )
18X-RAY DIFFRACTION18chain 'D' and (resid 70 through 88 )
19X-RAY DIFFRACTION19chain 'D' and (resid 89 through 142 )
20X-RAY DIFFRACTION20chain 'D' and (resid 143 through 262 )
21X-RAY DIFFRACTION21chain 'E' and (resid 3 through 51 )
22X-RAY DIFFRACTION22chain 'E' and (resid 52 through 69 )
23X-RAY DIFFRACTION23chain 'E' and (resid 70 through 88 )
24X-RAY DIFFRACTION24chain 'E' and (resid 89 through 142 )
25X-RAY DIFFRACTION25chain 'E' and (resid 143 through 202 )
26X-RAY DIFFRACTION26chain 'E' and (resid 203 through 263 )
27X-RAY DIFFRACTION27chain 'F' and (resid 4 through 65 )
28X-RAY DIFFRACTION28chain 'F' and (resid 66 through 85 )
29X-RAY DIFFRACTION29chain 'F' and (resid 86 through 129 )
30X-RAY DIFFRACTION30chain 'F' and (resid 130 through 261 )

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