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- PDB-6mn0: Crystal structure of meta-AAC0038, an environmental aminoglycosid... -

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Basic information

Entry
Database: PDB / ID: 6mn0
TitleCrystal structure of meta-AAC0038, an environmental aminoglycoside resistance enzyme, H168A mutant in complex with acetyl-CoA
ComponentsAminoglycoside N(3)-acetyltransferase
KeywordsTRANSFERASE / ANTIBIOTIC_NAT FAMILY / ACETYLTRANSFERASE / AMINOGLYCOSIDE / ANTIBIOTIC RESISTANCE / METAGENOME / SOIL / COENZYME A / gentamicin / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / National Institute of Allergy and Infectious Diseases / NIAID
Function / homologyaminoglycoside 3-N-acetyltransferase activity / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic / ACETYL COENZYME *A / Chem-PE3 / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsStogios, P.J. / Skarina, T. / Zu, X. / 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 1.2Apr 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 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)184,44649
Polymers171,9266
Non-polymers12,52043
Water29,6351645
1
A: Aminoglycoside N(3)-acetyltransferase
B: Aminoglycoside N(3)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,70916
Polymers57,3092
Non-polymers5,40114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Aminoglycoside N(3)-acetyltransferase
F: Aminoglycoside N(3)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,03716
Polymers57,3092
Non-polymers3,72814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Aminoglycoside N(3)-acetyltransferase
E: Aminoglycoside N(3)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,69917
Polymers57,3092
Non-polymers3,39115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.078, 159.620, 143.321
Angle α, β, γ (deg.)90.00, 94.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-597-

HOH

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Aminoglycoside N(3)-acetyltransferase


Mass: 28654.350 Da / Num. of mol.: 6 / Mutation: H168A
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

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Non-polymers , 6 types, 1688 molecules

#2: Chemical
ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C28H58O15
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1645 / 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: 3.59 Å3/Da / Density % sol: 65.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2 M ammonium sulfate, 0.1 M bis-Tris pH 5.5, 10 mM Neomycin

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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: Sep 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 94732 / % possible obs: 99.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.062 / Net I/σ(I): 10.75
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.09 / Num. unique obs: 4670 / Rpim(I) all: 0.249 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_3092: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HT0

5ht0


Resolution: 2.4→24.931 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.59
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 1996 2.11 %RANDOM
Rwork0.1781 ---
obs0.1787 94715 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→24.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12012 0 542 1645 14199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512842
X-RAY DIFFRACTIONf_angle_d1.7717463
X-RAY DIFFRACTIONf_dihedral_angle_d21.1344758
X-RAY DIFFRACTIONf_chiral_restr0.181860
X-RAY DIFFRACTIONf_plane_restr0.0042243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3928-2.45260.2891340.23126275X-RAY DIFFRACTION94
2.4526-2.51890.24511390.22516624X-RAY DIFFRACTION100
2.5189-2.59290.28461430.21396643X-RAY DIFFRACTION100
2.5929-2.67650.25671440.21656639X-RAY DIFFRACTION100
2.6765-2.77210.23921450.21196617X-RAY DIFFRACTION100
2.7721-2.88290.23051410.2026624X-RAY DIFFRACTION100
2.8829-3.01390.22211430.20666708X-RAY DIFFRACTION100
3.0139-3.17250.24521390.20026604X-RAY DIFFRACTION100
3.1725-3.37080.19741440.17646639X-RAY DIFFRACTION100
3.3708-3.63040.18341440.1596641X-RAY DIFFRACTION100
3.6304-3.99440.18291440.14686673X-RAY DIFFRACTION100
3.9944-4.56930.15181440.13776671X-RAY DIFFRACTION100
4.5693-5.74520.18191460.15546667X-RAY DIFFRACTION100
5.7452-24.93190.2141460.18276694X-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)
15.6821.61660.97925.2112-0.7983.5747-0.0059-0.0661-0.0890.09930.06390.23770.0547-0.2553-0.06750.15190.02040.01520.1276-0.02510.1434-117.214426.3474299.4358
26.0071-2.43881.94074.8007-0.23762.6525-0.5369-0.60120.16590.8470.4513-0.5694-0.3610.26630.13770.2346-0.02830.01460.2845-0.00330.2125-94.488221.7612300.9867
30.99-0.1581-0.25411.240.40830.30570.0122-0.11810.07260.08220.0225-0.1845-0.04520.0924-0.04040.2327-0.0162-0.02340.2410.00520.2199-96.049431.6797300.5593
45.5526-1.53260.48252.3506-0.15051.8824-0.0496-0.2265-0.06130.04440.085-0.0743-0.02450.0209-0.03910.1931-0.00220.00720.1310.03210.1219-99.73590.0495301.0092
51.1237-0.4410.31571.4825-0.60880.562-0.0114-0.0719-0.13780.00960.05380.15550.0853-0.032-0.0480.23680.00350.0050.1989-0.02320.2074-113.8487-6.7422299.4465
63.8706-1.00720.17734.3484-1.23974.69230.0680.20380.0096-0.11040.0220.2396-0.2929-0.2512-0.07990.1334-0.03030.00770.18020.02020.1702-120.208843.5943258.3239
75.576-6.8525-1.97919.55311.19352.4521-0.0362-0.0544-1.1344-0.178-0.19940.09810.75390.27650.26170.48790.03570.03360.34480.0560.3799-90.981626.5588260.0179
81.22450.0399-0.25810.9626-0.52481.1139-0.002-0.0052-0.07440.0203-0.0439-0.06890.0870.03350.04210.2322-0.0273-0.00130.209-0.01660.1993-109.543730.3263269.4783
93.8624-1.43070.33515.09370.55025.0699-0.03230.0602-0.0214-0.07740.07-0.2420.12230.3828-0.03250.1178-0.0278-0.01630.1541-0.01750.1619-83.8382-19.6681261.9289
105.651-5.05485.04097.84-1.85667.3615-0.29460.12581.5107-0.5391-0.4398-0.3079-1.7322-0.19740.75040.68330.0344-0.05770.4113-0.02490.488-110.3081-1.0644258.6419
111.2830.0756-0.19221.49260.89961.57740.0203-0.00230.1062-0.0636-0.01250.0142-0.1935-0.0289-0.00710.2060.00190.01150.17680.02350.1553-96.1276-5.8959270.5076
124.74581.2596-0.5793.42961.55573.6860.0984-0.08290.33440.0533-0.20110.273-0.205-0.49190.09410.20220.0384-0.04020.3032-0.00940.1632-115.2978-16.2716244.941
138.9216-4.86780.16063.5310.65850.68510.18310.9880.3632-0.0977-0.2499-0.3174-0.04830.24940.0940.3348-0.0025-0.00160.38830.02560.2997-83.9655-28.9626244.2609
141.1014-0.1890.55961.25410.1082.351-0.00160.1607-0.0656-0.1782-0.00310.06380.1373-0.0472-0.00110.2322-0.0520.0140.2333-0.0060.1737-103.2601-29.7016235.8155
154.92610.89451.15633.6853-1.84894.3578-0.0174-0.1859-0.27270.0155-0.133-0.31390.25110.4550.14430.19950.02780.07730.2880.02360.1785-86.031340.9636247.0315
167.7133-3.89173.31265.7522-3.20455.11610.1320.7703-0.3935-0.2370.0350.68440.1686-0.2607-0.16280.3031-0.0219-0.00090.26140.00060.3213-117.145853.1115241.0216
171.1836-0.1705-0.46021.1821-0.37091.97190.03190.13690.0792-0.1747-0.0091-0.0915-0.11760.0541-0.02680.2348-0.05530.00830.22090.00350.1778-96.705554.445236.0523
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 263 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 74 )
5X-RAY DIFFRACTION5chain 'B' and (resid 75 through 263 )
6X-RAY DIFFRACTION6chain 'C' and (resid 2 through 62 )
7X-RAY DIFFRACTION7chain 'C' and (resid 63 through 80 )
8X-RAY DIFFRACTION8chain 'C' and (resid 81 through 262 )
9X-RAY DIFFRACTION9chain 'D' and (resid 3 through 62 )
10X-RAY DIFFRACTION10chain 'D' and (resid 63 through 77 )
11X-RAY DIFFRACTION11chain 'D' and (resid 78 through 262 )
12X-RAY DIFFRACTION12chain 'E' and (resid 4 through 62 )
13X-RAY DIFFRACTION13chain 'E' and (resid 63 through 80 )
14X-RAY DIFFRACTION14chain 'E' and (resid 81 through 263 )
15X-RAY DIFFRACTION15chain 'F' and (resid 3 through 62 )
16X-RAY DIFFRACTION16chain 'F' and (resid 63 through 80 )
17X-RAY DIFFRACTION17chain 'F' and (resid 81 through 263 )

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