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- PDB-5f48: Crystal structure of an aminoglycoside acetyltransferase meta-AAC... -

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Basic information

Entry
Database: PDB / ID: 5f48
TitleCrystal structure of an aminoglycoside acetyltransferase meta-AAC0020 from an uncultured soil metagenomic sample in complex with coenzyme A
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: 1.95 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 30, 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 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)38,6978
Polymers37,0542
Non-polymers1,6436
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-61 kcal/mol
Surface area15140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.133, 80.187, 53.926
Angle α, β, γ (deg.)90.00, 91.97, 90.00
Int Tables number4
Space group name H-MP1211

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 9% PEG 8000, 0.2 M calcium acetate hydrate, 0.1 M sodium cacodylate, 20 mM gentamicin, 20 acetyl-CoA

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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: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 27961 / % possible obs: 97.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 25.85
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.611 / % possible all: 96.2

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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: apoenzyme

Resolution: 1.95→23.621 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 1403 5.02 %Random selection
Rwork0.1895 ---
obs0.1918 27937 97.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→23.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 0 100 405 3027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182711
X-RAY DIFFRACTIONf_angle_d1.2433672
X-RAY DIFFRACTIONf_dihedral_angle_d20.1651078
X-RAY DIFFRACTIONf_chiral_restr0.047383
X-RAY DIFFRACTIONf_plane_restr0.006459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9503-2.020.36031350.31072554X-RAY DIFFRACTION94
2.02-2.10080.31881360.27282633X-RAY DIFFRACTION96
2.1008-2.19640.27851390.22272627X-RAY DIFFRACTION97
2.1964-2.31210.24641420.19892633X-RAY DIFFRACTION97
2.3121-2.45680.23721470.19412632X-RAY DIFFRACTION98
2.4568-2.64620.26051390.19422674X-RAY DIFFRACTION98
2.6462-2.91210.25031440.19722668X-RAY DIFFRACTION98
2.9121-3.33250.24231390.18492694X-RAY DIFFRACTION99
3.3325-4.19480.18831410.15772696X-RAY DIFFRACTION98
4.1948-23.62320.20891410.17052723X-RAY DIFFRACTION98
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)
11.19470.78660.28596.03262.85981.36260.62790.3668-1.1167-0.9044-0.4584-0.8152.34340.0041-0.23051.38160.3402-0.12140.94830.13920.552219.82912.879229.8303
23.8304-0.1339-0.36336.0563-0.83393.29520.0317-0.13380.03270.27440.0150.0642-0.21670.064-0.02680.2082-0.01240.01090.1903-0.01660.12312.647713.914822.088
35.08292.41131.58142.93980.93653.69520.0698-0.0811-0.13140.0782-0.0053-0.08330.04760.2766-0.0850.16930.04960.01570.249-0.01780.1956.03744.170611.5321
47.4817-3.64083.57642.7623-3.13283.8747-0.14230.21040.29950.1083-0.1144-0.2809-0.1640.5390.2570.2473-0.04880.02160.303-0.03640.234710.374612.65051.7474
54.4675-0.7324-0.75563.59960.92685.3667-0.01130.0059-0.14310.0644-0.03460.05380.3008-0.23450.04570.1996-0.0554-0.01970.1875-0.01090.2107-15.14261.9574-4.4955
63.0563.61232.07865.76384.30323.6680.1028-0.25020.10710.1444-0.36950.1232-0.0028-0.67910.36410.22060.0610.03140.26330.01440.2445-10.26112.46292.7505
73.42110.0289-1.01511.79710.56767.1282-0.00790.0491-0.0241-0.05750.0723-0.1263-0.10180.2404-0.05710.18230.0002-0.00310.11070.02050.1709-6.640614.1065-7.9306
81.4684-1.2496-0.31484.3132-1.6842.23560.14220.1826-0.0658-0.4731-0.04990.08790.14920.1754-0.08910.2171-0.0354-0.07280.3009-0.02650.24636.54689.8295-0.2277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 8:10)
2X-RAY DIFFRACTION2(chain A and resid 11:73)
3X-RAY DIFFRACTION3(chain A and resid 74:128)
4X-RAY DIFFRACTION4(chain A and resid 129:157)
5X-RAY DIFFRACTION5(chain B and resid 7:64)
6X-RAY DIFFRACTION6(chain B and resid 65:85)
7X-RAY DIFFRACTION7(chain B and resid 86:141)
8X-RAY DIFFRACTION8(chain B and resid 142:157)

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