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- PDB-5f49: Crystal structure of an aminoglycoside acetyltransferase meta-AAC... -

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Basic information

Entry
Database: PDB / ID: 5f49
TitleCrystal structure of an aminoglycoside acetyltransferase meta-AAC0020 from an uncultured soil metagenomic sample in complex with malonyl-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


spermidine acetylation / spermidine binding / diamine N-acetyltransferase activity / metal ion binding / cytoplasm
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
COENZYME A / MALONYL-COENZYME A / AAC3-I
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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 1.3Mar 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_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_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_label_seq_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
C: aminoglycoside acetyltransferase meta-AAC0020
D: aminoglycoside acetyltransferase meta-AAC0020
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,63116
Polymers74,1084
Non-polymers3,52312
Water7,386410
1
A: aminoglycoside acetyltransferase meta-AAC0020
B: aminoglycoside acetyltransferase meta-AAC0020
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7979
Polymers37,0542
Non-polymers1,7437
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-77 kcal/mol
Surface area16200 Å2
MethodPISA
2
C: aminoglycoside acetyltransferase meta-AAC0020
D: aminoglycoside acetyltransferase meta-AAC0020
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8347
Polymers37,0542
Non-polymers1,7805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-73 kcal/mol
Surface area14590 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18210 Å2
ΔGint-160 kcal/mol
Surface area29430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.159, 54.047, 84.847
Angle α, β, γ (deg.)72.30, 74.57, 88.07
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
aminoglycoside acetyltransferase meta-AAC0020


Mass: 18526.986 Da / Num. of mol.: 4
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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MLC / MALONYL-COENZYME A


Mass: 853.580 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H38N7O19P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 18% PEG 8000, 0.2 M calcium acetate hydrate, 0.1 M sodium cacodylate
PH range: 7

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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: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→25 Å / Num. obs: 39176 / % possible obs: 95.6 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 16.96
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.577 / % possible all: 92.9

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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: 2.15→23.487 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 1958 5 %Random selection
Rwork0.1922 ---
obs0.1939 39170 95.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→23.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4996 0 218 410 5624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085339
X-RAY DIFFRACTIONf_angle_d1.9297261
X-RAY DIFFRACTIONf_dihedral_angle_d16.1061991
X-RAY DIFFRACTIONf_chiral_restr0.13790
X-RAY DIFFRACTIONf_plane_restr0.005907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1477-2.20140.27961310.27092550X-RAY DIFFRACTION91
2.2014-2.26090.34161400.26122648X-RAY DIFFRACTION94
2.2609-2.32740.28421350.24442601X-RAY DIFFRACTION94
2.3274-2.40240.28471430.24252610X-RAY DIFFRACTION94
2.4024-2.48820.29351330.23892641X-RAY DIFFRACTION95
2.4882-2.58770.31370.22692656X-RAY DIFFRACTION95
2.5877-2.70530.24911450.22372643X-RAY DIFFRACTION95
2.7053-2.84770.26341360.22212646X-RAY DIFFRACTION96
2.8477-3.02580.23881440.2112690X-RAY DIFFRACTION96
3.0258-3.25880.26511430.20092672X-RAY DIFFRACTION97
3.2588-3.58570.2241470.17842691X-RAY DIFFRACTION97
3.5857-4.10220.19281330.16562727X-RAY DIFFRACTION98
4.1022-5.15930.15341450.1342709X-RAY DIFFRACTION98
5.1593-23.48870.18881460.17752728X-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)
13.42420.1890.61342.7161-1.35345.21330.0128-0.17780.3550.0354-0.08250.0525-0.1516-0.19050.07620.22670.01010.02540.0874-0.04860.237-43.7474-14.7895-23.1666
22.5596-0.24770.33132.51770.84152.07750.05950.13350.3489-0.0652-0.10730.0637-0.1892-0.13990.02520.19770.0089-0.02020.15370.05280.2443-41.4904-20.8802-29.9893
36.20981.0638-3.5592.44380.16926.70580.0240.07230.1484-0.3315-0.03320.25770.07580.22640.00510.17410.0149-0.05170.13740.00010.1879-46.478-26.5501-35.6214
46.1166-1.79064.00473.322-1.8633.6515-0.0705-0.2760.17020.14220.03470.3322-0.0741-0.19770.00640.2315-0.02270.04010.16320.00820.2581-48.1919-35.6438-26.5637
56.04771.06991.43353.72620.48813.39810.02240.2862-0.3289-0.13340.0593-0.10810.262-0.0469-0.05810.26750.0330.04590.1858-0.05430.176-23.7264-44.9671-37.5718
61.9977-0.4115-0.4812.804-0.22531.2369-0.00960.1512-0.1865-0.27090-0.05010.0658-0.01840.00650.1729-0.0044-0.01660.15560.01270.1643-26.6619-39.5105-30.7291
71.5152.0156-0.5546.86831.59311.4991-0.0092-0.2728-0.14580.14290.0819-0.05490.13270.0149-0.0620.24110.0164-0.00110.14110.07140.1475-30.3583-40.8856-22.0824
82.611-0.7207-0.0261.7557-0.24480.0410.1072-0.1409-0.38490.03570.08080.38970.1535-0.0935-0.1430.25530.00610.0040.11220.00260.2664-42.3254-43.0136-26.6524
95.9096-0.16631.23427.29822.09634.33420.1825-0.09770.29580.1301-0.20510.0467-0.91040.47220.03840.3905-0.13920.04060.4462-0.01370.2032-25.1922-11.4729-1.855
102.293-0.1265-0.76832.0784-0.85992.91910.2484-0.38180.24290.0723-0.2266-0.0972-0.55720.4988-0.03930.3163-0.0818-0.00330.5055-0.12890.2913-26.452-14.38317.1801
115.1334-0.8335-0.81591.6571-1.74492.55190.0519-0.21610.18660.1315-0.0269-0.071-0.39540.5612-0.03280.2986-0.0866-0.06190.6386-0.09570.2802-21.5544-17.773314.3906
126.30252.51633.41472.48111.14091.8718-0.16490.2101-0.31670.00330.1188-0.3209-0.05260.55610.02280.32180.05660.04350.6958-0.06290.3385-19.8465-29.47638.8985
133.3985-1.01221.09926.15350.64025.9205-0.039-0.1384-0.11180.4627-0.0099-0.07130.83790.09930.03820.3807-0.0070.03990.48020.03860.2071-43.8044-33.576823.0653
143.02540.5217-1.35433.1146-0.52494.8176-0.1353-0.3236-0.36660.13550.06790.00060.42-0.12030.04640.21450.0113-0.01810.3709-0.02150.2355-41.1754-31.617313.897
154.13460.1393-1.06746.2175-2.20963.7258-0.26340.0856-0.35210.03840.1143-0.1270.38040.02570.15810.37770.00730.03070.3653-0.12150.2275-37.4697-35.89826.4902
165.02933.08712.1057.76713.96726.1799-0.0377-0.1605-0.82630.70140.0339-0.15781.04120.8368-0.05860.42340.16720.06120.51090.04580.4387-25.6387-36.08911.4337
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 8 through 44
2X-RAY DIFFRACTION2chain A and resid 45 through 102
3X-RAY DIFFRACTION3chain A and resid 103 through 131
4X-RAY DIFFRACTION4chain A and resid 132 through 157
5X-RAY DIFFRACTION5chain B and resid 8 through 44
6X-RAY DIFFRACTION6chain B and resid 45 through 102
7X-RAY DIFFRACTION7chain B and resid 103 through 131
8X-RAY DIFFRACTION8chain B and resid 132 through 157
9X-RAY DIFFRACTION9chain C and resid 10 through 44
10X-RAY DIFFRACTION10chain C and resid 45 through 102
11X-RAY DIFFRACTION11chain C and resid 103 through 131
12X-RAY DIFFRACTION12chain C and resid 132 through 157
13X-RAY DIFFRACTION13chain D and resid 10 through 44
14X-RAY DIFFRACTION14chain D and resid 45 through 102
15X-RAY DIFFRACTION15chain D and resid 103 through 131
16X-RAY DIFFRACTION16chain D and resid 132 through 157

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