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- PDB-6mn2: Crystal structure of meta-AAC0038, an environmental aminoglycosid... -

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Basic information

Entry
Database: PDB / ID: 6mn2
TitleCrystal structure of meta-AAC0038, an environmental aminoglycoside resistance enzyme, mutant H168A in abortive complex with sisomicin-CoA
ComponentsAminoglycoside N(3)-acetyltransferase
KeywordsTRANSFERASE/ANTIBIOTIC / ANTIBIOTIC_NAT FAMILY / ACETYLTRANSFERASE / AMINOGLYCOSIDE / ANTIBIOTIC RESISTANCE / METAGENOME / SOIL / COENZYME A / sisomicin / CSGID / TRANSFERASE / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / National Institute of Allergy and Infectious Diseases / NIAID / TRANSFERASE-ANTIBIOTIC complex
Function / homology
Function and homology information


aminoglycoside 3-N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic
Similarity search - Function
Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like
Similarity search - Domain/homology
COENZYME A / DI(HYDROXYETHYL)ETHER / Chem-SIS / Aminoglycoside N(3)-acetyltransferase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.744 Å
AuthorsStogios, P.J. / Skarina, T. / Michalska, K. / 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: To Be Published
Title: Crystal structure of meta-AAC0038, an environmental aminoglycoside resistance enzyme, mutant H168A in abortive complex with sisomicin-CoA
Authors: Stogios, P.J.
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 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,15312
Polymers57,3092
Non-polymers2,84510
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-25 kcal/mol
Surface area22870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.755, 127.755, 95.114
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aminoglycoside N(3)-acetyltransferase


Mass: 28654.350 Da / Num. of mol.: 2 / 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, 130 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-SIS / (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside / Sisomicin


Mass: 447.526 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H37N5O7 / Comment: antibiotic*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.91 Å3/Da / Density % sol: 68.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium sulfate, 0.1 M sodium cacodylate pH 6.5, 30% PEG 8K, 10 mM sisomicin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 23797 / % possible obs: 100 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.289 / Rpim(I) all: 0.08 / Net I/σ(I): 11.7
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 13.3 % / Rmerge(I) obs: 2.209 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 1183 / CC1/2: 0.708 / Rpim(I) all: 0.626 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HT0

5ht0


Resolution: 2.744→29.204 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2699 2267 5.01 %RANDOM
Rwork0.2492 ---
obs0.2503 45290 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.744→29.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3987 0 180 120 4287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154267
X-RAY DIFFRACTIONf_angle_d1.0865813
X-RAY DIFFRACTIONf_dihedral_angle_d23.3731597
X-RAY DIFFRACTIONf_chiral_restr0.049609
X-RAY DIFFRACTIONf_plane_restr0.006745
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7443-2.8040.38311400.36412674X-RAY DIFFRACTION99
2.804-2.86910.36971420.36942723X-RAY DIFFRACTION100
2.8691-2.94080.40221440.3572679X-RAY DIFFRACTION100
2.9408-3.02030.35121380.33892657X-RAY DIFFRACTION100
3.0203-3.1090.3211500.31542729X-RAY DIFFRACTION100
3.109-3.20930.31951420.30142676X-RAY DIFFRACTION100
3.2093-3.32380.3321380.29312715X-RAY DIFFRACTION100
3.3238-3.45670.27011440.29832702X-RAY DIFFRACTION100
3.4567-3.61370.31861340.28662672X-RAY DIFFRACTION100
3.6137-3.80390.30291450.29572669X-RAY DIFFRACTION99
3.8039-4.04160.27341310.27032640X-RAY DIFFRACTION98
4.0416-4.35280.23251440.19772699X-RAY DIFFRACTION100
4.3528-4.78910.19781370.18092709X-RAY DIFFRACTION100
4.7891-5.47810.22571430.17532713X-RAY DIFFRACTION100
5.4781-6.88690.20331460.1922673X-RAY DIFFRACTION100
6.8869-29.20520.20031490.17962693X-RAY DIFFRACTION100
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)
11.4025-1.35270.5666.0951-0.05184.13840.01730.07650.0703-0.2384-0.0834-0.30620.23910.09450.05890.1423-0.0326-0.00730.29150.00740.2237211.8635277.0982-0.9842
26.3821-0.84081.60890.93410.93874.4593-0.23360.5590.42020.56440.3178-0.2041-0.9704-1.2057-0.13580.32350.08930.10670.56930.19320.4974181.9772288.48292.2252
33.28090.83220.030.29890.08143.253-0.0265-0.2172-0.05920.09740.11270.1491-0.2145-0.3598-0.08320.21820.01750.03450.27350.05980.2932194.5652276.92995.5635
45.13290.19840.31460.69690.5082.98730.2203-0.7850.50880.2199-0.03750.0196-0.3106-0.1926-0.17320.3278-0.02680.05620.31850.01440.381196.5888283.698616.8132
51.67650.8518-0.49764.1770.36063.5018-0.00340.29840.28820.058-0.09540.6783-0.1701-0.68110.10580.23880.0362-0.00320.74870.20090.5178181.4303285.3245-18.7513
65.46781.22830.67781.854-0.23473.48220.04350.5140.4885-0.04770.0906-0.1563-0.15110.3371-0.13050.2958-0.00960.03240.3712-0.00330.352213.1911279.1878-19.6089
72.1406-1.1414-0.5491.42160.10553.3140.19440.89590.2569-0.3628-0.102-0.0281-0.1257-0.4842-0.11550.3434-0.0598-0.00510.61830.11270.3452197.4164279.4389-28.5739
82.5632-0.2157-0.08242.4317-0.4491.830.19370.90790.5852-0.43360.3855-0.155-0.0124-0.2653-0.3090.4935-0.04730.27930.51350.27330.5997208.6019281.6903-31.6443
96.2397-1.4298-3.23941.86991.92692.58040.02410.46970.1388-0.2524-0.4757-0.0961-0.7552-0.18780.36840.62190.16670.05261.06470.47110.768184.408294.9826-33.4103
101.5303-0.7786-0.00012.79940.17370.01980.24941.49890.7335-0.69440.1405-0.1488-0.2031-0.58270.14570.72410.154-0.00341.55370.43820.557191.0655289.8392-41.6935
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 76 )
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 173 )
4X-RAY DIFFRACTION4chain 'A' and (resid 174 through 262 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 62 )
6X-RAY DIFFRACTION6chain 'B' and (resid 63 through 87 )
7X-RAY DIFFRACTION7chain 'B' and (resid 88 through 189 )
8X-RAY DIFFRACTION8chain 'B' and (resid 190 through 215 )
9X-RAY DIFFRACTION9chain 'B' and (resid 216 through 236 )
10X-RAY DIFFRACTION10chain 'B' and (resid 237 through 261 )

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