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- PDB-5f46: Crystal structure of an aminoglycoside acetyltransferase meta-AAC... -

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Basic information

Entry
Database: PDB / ID: 5f46
TitleCrystal structure of an aminoglycoside acetyltransferase meta-AAC0020 from an uncultured soil metagenomic sample, apoenzyme form
Componentsaminoglycoside acetyltransferase meta-AAC0020
KeywordsTRANSFERASE / GNAT fold / GCN5-N-acetyltransferase fold / acetyltransferase / aminoglycoside / antibiotic resistance / metagenome / soil / coenzyme A / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / metal ion binding
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsXu, Z. / Skarina, T. / Stogios, P.J. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: ACS Infect Dis / Year: 2017
Title: Structural and Functional Survey of Environmental Aminoglycoside Acetyltransferases Reveals Functionality of Resistance Enzymes.
Authors: Xu, Z. / Stogios, P.J. / Quaile, A.T. / Forsberg, K.J. / Patel, S. / Skarina, T. / Houliston, S. / Arrowsmith, C. / Dantas, G. / Savchenko, A.
History
DepositionDec 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Structure summary
Revision 1.2Apr 3, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_database_related / pdbx_struct_oper_list / struct
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 / _entity.pdbx_description / _pdbx_struct_oper_list.symmetry_operation / _struct.pdbx_descriptor / _struct.title
Revision 1.3Sep 27, 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 acetyltransferase meta-AAC0020
B: aminoglycoside acetyltransferase meta-AAC0020
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1254
Polymers37,0542
Non-polymers712
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-52 kcal/mol
Surface area15070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.850, 61.807, 114.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein aminoglycoside acetyltransferase meta-AAC0020


Mass: 18526.986 Da / Num. of mol.: 2
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) / References: UniProt: A0A059WZ16
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 4 M sodium formate

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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: Feb 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 33193 / % possible obs: 97.2 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 0.577
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.405 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YFJ

4yfj


Resolution: 1.85→29.842 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 1592 4.99 %Random selection
Rwork0.2086 ---
obs0.2107 31885 93.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→29.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 0 2 354 2878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042605
X-RAY DIFFRACTIONf_angle_d0.7813533
X-RAY DIFFRACTIONf_dihedral_angle_d14.16961
X-RAY DIFFRACTIONf_chiral_restr0.033383
X-RAY DIFFRACTIONf_plane_restr0.004454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8493-1.9090.30191270.27832479X-RAY DIFFRACTION86
1.909-1.97720.28341340.25042562X-RAY DIFFRACTION88
1.9772-2.05630.22711370.23322648X-RAY DIFFRACTION91
2.0563-2.14990.26351420.22272643X-RAY DIFFRACTION92
2.1499-2.26320.26691400.22932705X-RAY DIFFRACTION93
2.2632-2.4050.28441450.22742730X-RAY DIFFRACTION93
2.405-2.59060.28191490.23822768X-RAY DIFFRACTION94
2.5906-2.85110.29041500.24652855X-RAY DIFFRACTION97
2.8511-3.26320.29691530.21932943X-RAY DIFFRACTION99
3.2632-4.10960.20991540.1742908X-RAY DIFFRACTION97
4.1096-29.84560.23291610.18953052X-RAY DIFFRACTION97
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)
17.39245.5585-5.84074.7907-3.91896.23420.18430.96640.2636-0.12160.556-0.506-2.0919-0.5772-0.71811.2563-0.14290.18010.5166-0.0690.540236.877150.22478.2631
21.61530.1115-0.3832.5879-0.19087.2913-0.00050.2226-0.0467-0.40410.0960.0054-0.27720.0178-0.09040.2842-0.01310.01720.2231-0.02910.250534.266134.630614.8031
32.5141-2.1832-0.24371.910.51735.39240.14820.23890.2687-0.42260.0822-0.47-0.85920.8362-0.15740.5571-0.24750.0820.4702-0.07380.341444.566642.663413.5841
41.4178-0.3249-0.46333.35120.46121.0033-0.04990.03020.1435-0.51420.4097-0.9209-0.17110.5121-0.30570.3297-0.11120.08480.4897-0.18030.423946.434837.673124.6979
59.7754.8021-3.11835.0491-4.53524.54080.7156-0.6264-1.882-0.0315-1.0522-0.45782.21030.8410.35321.00580.0931-0.13310.51410.06750.704936.245511.716848.26
65.1846-0.11811.43155.6598-0.63573.76870.0701-0.34580.29460.8137-0.04610.2242-0.1730.0592-0.02960.3820.03820.05650.257-0.0340.180631.314429.656843.3138
71.0390.36181.51742.8218-2.82056.2960.009-0.0665-0.01380.1878-0.0362-0.20740.43060.39390.0270.3620.1393-0.01650.3347-0.04460.309139.020922.138936.0288
81.4843-0.73090.44553.2293-0.09151.0985-0.0952-0.01330.0650.5080.3646-1.06360.09960.6263-0.23470.33290.1072-0.07660.5452-0.18060.510346.249526.395531.0359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 8:15)
2X-RAY DIFFRACTION2(chain A and resid 16:86)
3X-RAY DIFFRACTION3(chain A and resid 87:111)
4X-RAY DIFFRACTION4(chain A and resid 112:157)
5X-RAY DIFFRACTION5(chain B and resid 7:14)
6X-RAY DIFFRACTION6(chain B and resid 15:65)
7X-RAY DIFFRACTION7(chain B and resid 66:113)
8X-RAY DIFFRACTION8(chain B and resid 114:157)

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