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- PDB-5f47: Crystal structure of an aminoglycoside acetyltransferase meta-AAC... -

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Basic information

Entry
Database: PDB / ID: 5f47
TitleCrystal structure of an aminoglycoside acetyltransferase meta-AAC0020 from an uncultured soil metagenomic sample in complex with trehalose
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.497 Å
AuthorsXu, Z. / Skarina, T. / Wawrzak, Z. / 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 1.2Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 3, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_database_related / 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 / _struct.pdbx_descriptor / _struct.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _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_alt_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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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_alt_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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)37,78813
Polymers37,0542
Non-polymers73411
Water12,178676
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-122 kcal/mol
Surface area15360 Å2
MethodPISA
2
A: aminoglycoside acetyltransferase meta-AAC0020
B: aminoglycoside acetyltransferase meta-AAC0020
hetero molecules

A: aminoglycoside acetyltransferase meta-AAC0020
B: aminoglycoside acetyltransferase meta-AAC0020
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,57626
Polymers74,1084
Non-polymers1,46822
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area17350 Å2
ΔGint-273 kcal/mol
Surface area28400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.001, 53.954, 46.023
Angle α, β, γ (deg.)90.00, 105.19, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-479-

HOH

21A-509-

HOH

31A-611-

HOH

41B-378-

HOH

51B-391-

HOH

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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: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 676 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3350, 0.2 M calcium chloride, 10 mM neomycin, 2% trehalose, paratone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.497→30 Å / Num. obs: 51615 / % possible obs: 96.8 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 32.39
Reflection shellResolution: 1.497→1.53 Å / Redundancy: 4 % / % possible all: 93.6

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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: 1.497→26.977 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1776 1999 3.88 %Random selection
Rwork0.1557 ---
obs0.1566 51548 96.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.497→26.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2539 0 33 676 3248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082659
X-RAY DIFFRACTIONf_angle_d1.1393613
X-RAY DIFFRACTIONf_dihedral_angle_d14.157980
X-RAY DIFFRACTIONf_chiral_restr0.048401
X-RAY DIFFRACTIONf_plane_restr0.006460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.497-1.53410.23981320.22773255X-RAY DIFFRACTION89
1.5341-1.57560.25451320.20723478X-RAY DIFFRACTION96
1.5756-1.6220.21121470.19633489X-RAY DIFFRACTION96
1.622-1.67430.21041490.1853492X-RAY DIFFRACTION96
1.6743-1.73410.20421360.17983502X-RAY DIFFRACTION96
1.7341-1.80350.23061390.18963518X-RAY DIFFRACTION96
1.8035-1.88560.20151530.17663519X-RAY DIFFRACTION97
1.8856-1.9850.17791420.16053558X-RAY DIFFRACTION97
1.985-2.10930.17981440.15893555X-RAY DIFFRACTION97
2.1093-2.27210.20551370.15883604X-RAY DIFFRACTION98
2.2721-2.50060.17821520.15753585X-RAY DIFFRACTION98
2.5006-2.86210.18291410.15933637X-RAY DIFFRACTION98
2.8621-3.60460.15531420.14043632X-RAY DIFFRACTION99
3.6046-26.98140.15121530.13423725X-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)
16.01191.7316-2.81195.3244-5.94237.3269-0.02890.75630.9517-0.51450.13420.2598-1.2099-0.3027-0.12590.5057-0.0602-0.08090.33480.14040.30026.701437.141131.7157
21.9337-0.03640.5851.98740.94863.5433-0.07770.20920.08-0.04060.1575-0.224-0.06520.5338-0.08980.1325-0.03080.0170.2562-0.01420.165518.978627.23144.2381
32.18310.90890.48333.1552-0.45562.0318-0.06940.12030.1454-0.07230.0365-0.0678-0.19860.05650.01190.1294-0.00320.01430.13-0.00440.10983.875227.123542.4842
41.2197-1.05180.15612.082-0.7722.0758-0.1996-0.19420.31130.22860.1269-0.0957-0.4769-0.18840.08930.20230.0013-0.00440.1325-0.02820.180.550430.793556.9773
54.4034-4.71373.15319.66171.28436.9763-0.9836-1.9386-0.4912.35230.714-0.13120.06340.67810.22240.9934-0.0706-0.2181.06290.35210.61981.9776-2.642677.681
62.8294-0.19810.5312.10230.24642.79550.03350.0125-0.48110.05730.032-0.03050.2909-0.161-0.0470.1893-0.0173-0.02370.12830.02070.2062-1.47493.020954.3148
73.04951.5-0.83492.912-1.79023.5140.0382-0.2172-0.220.10010.0189-0.0280.1518-0.067-0.03110.14420.0137-0.01320.1299-0.00290.12396.305710.348561.5308
81.1549-1.08821.6850.9259-1.17735.2794-0.0571-0.2264-0.14760.17160.17750.10880.0258-0.368-0.11660.1665-0.00540.02340.17260.0070.1505-1.528222.325463.0369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 7:15)
2X-RAY DIFFRACTION2(chain A and resid 16:54)
3X-RAY DIFFRACTION3(chain A and resid 55:126)
4X-RAY DIFFRACTION4(chain A and resid 127:157)
5X-RAY DIFFRACTION5(chain B and resid 6:9)
6X-RAY DIFFRACTION6(chain B and resid 10:61)
7X-RAY DIFFRACTION7(chain B and resid 62:126)
8X-RAY DIFFRACTION8(chain B and resid 127:157)

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