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- PDB-5u08: Crystal structure of an aminoglycoside acetyltransferase meta-AAC... -

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Basic information

Entry
Database: PDB / ID: 5u08
TitleCrystal structure of an aminoglycoside acetyltransferase meta-AAC0020 from an uncultured soil metagenomic sample in complex with sisomicin
Componentsaminoglycoside acetyltransferase meta-AAC0020
KeywordsTRANSFERASE/ANTIBIOTIC / GNAT fold / GCN5-N-acetyltransferase fold / acetyltransferase / aminoglycoside / sisomicin / antibiotic resistance / metagenome / soil / coenzyme A / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / TRANSFERASE-ANTIBIOTIC complex
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
ACETATE ION / Chem-SIS / AAC3-I
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
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
DepositionNov 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.2Apr 3, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / 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 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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)76,03920
Polymers73,7404
Non-polymers2,30016
Water17,493971
1
A: aminoglycoside acetyltransferase meta-AAC0020
B: aminoglycoside acetyltransferase meta-AAC0020
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,02710
Polymers36,8702
Non-polymers1,1588
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-51 kcal/mol
Surface area15800 Å2
MethodPISA
2
C: aminoglycoside acetyltransferase meta-AAC0020
D: aminoglycoside acetyltransferase meta-AAC0020
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,01210
Polymers36,8702
Non-polymers1,1428
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-68 kcal/mol
Surface area15750 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16290 Å2
ΔGint-142 kcal/mol
Surface area29860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.295, 53.035, 78.676
Angle α, β, γ (deg.)71.76, 75.61, 88.69
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
aminoglycoside acetyltransferase meta-AAC0020


Mass: 18434.891 Da / Num. of mol.: 4 / Mutation: Y138A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A059WZ16

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Non-polymers , 5 types, 987 molecules

#2: 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 / Sisomicin


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


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 971 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3350, 0.2 M calcium acetate, 20 mM sisomicin, soaked 24 hours in 20 mM sisomicin

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2016
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.52→19.55 Å / Num. obs: 102238 / % possible obs: 96.6 % / Redundancy: 15.6 % / CC1/2: 1 / Rmerge(I) obs: 0.067 / Net I/σ(I): 22.3
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.301 / Mean I/σ(I) obs: 2 / CC1/2: 0.799 / Rpim(I) all: 0.538 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5F46

5f46


Resolution: 1.52→19.547 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1998 1999 1.96 %Random selection
Rwork0.1659 ---
obs0.1665 102141 96.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→19.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5009 0 148 971 6128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155297
X-RAY DIFFRACTIONf_angle_d1.0477194
X-RAY DIFFRACTIONf_dihedral_angle_d23.5561932
X-RAY DIFFRACTIONf_chiral_restr0.359809
X-RAY DIFFRACTIONf_plane_restr0.007903
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.5580.29231320.30687000X-RAY DIFFRACTION94
1.558-1.60010.36831300.26987013X-RAY DIFFRACTION94
1.6001-1.64720.25861470.24227003X-RAY DIFFRACTION95
1.6472-1.70030.27371400.22227074X-RAY DIFFRACTION95
1.7003-1.76110.2111380.2097090X-RAY DIFFRACTION96
1.7611-1.83150.22681500.19457133X-RAY DIFFRACTION96
1.8315-1.91480.20231420.18417109X-RAY DIFFRACTION96
1.9148-2.01570.18081430.17147158X-RAY DIFFRACTION97
2.0157-2.14180.18671470.16697159X-RAY DIFFRACTION97
2.1418-2.30690.1831420.16187257X-RAY DIFFRACTION97
2.3069-2.53860.1761460.16157223X-RAY DIFFRACTION98
2.5386-2.9050.20781520.16737268X-RAY DIFFRACTION98
2.905-3.6560.19561430.14937312X-RAY DIFFRACTION99
3.656-19.54860.18571470.14057343X-RAY DIFFRACTION99
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)
11.5675-0.232-0.61870.49160.9662.9315-0.21640.25160.0988-0.3231-0.09760.3641-0.4189-1.0433-0.14360.38650.1323-0.10050.39380.01310.4497-53.6417-7.9066-37.5795
21.8707-0.09450.96481.35020.54471.5901-0.0573-0.05940.262-0.0293-0.0403-0.083-0.2383-0.121-0.03210.1558-0.0267-0.0020.04490.01760.1531-38.9473-16.1111-28.9307
30.35630.40350.01280.72650.01630.7053-0.0125-0.22350.0940.0037-0.12310.3327-0.0086-0.5136-0.00910.16670.01990.00520.2537-0.04610.2165-51.6453-18.5083-31.4616
41.7441-0.36630.76061.3639-0.17980.67010.03-0.1913-0.13-0.02550.00460.25380.0081-0.1930.00020.1721-0.02790.03480.1560.00390.1711-45.9596-29.8719-33.0574
50.04420.00080.0340.25240.14590.35880.3635-1.0042-1.07230.0882-0.2466-0.50230.87190.330.00770.42120.0533-0.11190.3140.0520.7261-15.0172-48.4954-28.3352
61.2806-0.2688-0.18361.3577-0.4131.97370.0790.2829-0.0969-0.23980.098-0.14770.04210.11860.00460.1679-0.0070.01120.1242-0.02650.2091-23.4935-37.2685-40.8754
71.35560.12540.39870.891-0.34381.36690.0045-0.0831-0.2347-0.01030.0907-0.12680.1827-0.00860.03860.1571-0.0394-0.00940.04630.02450.179-27.8143-38.9879-28.9551
81.7618-0.31740.04271.1727-0.37960.93280.0476-0.2953-0.58640.03480.1390.09510.2053-0.25590.01020.2084-0.05640.01180.12920.05820.2578-37.851-37.9496-27.6727
90.4028-0.18510.43890.1696-0.31880.5959-0.06080.3716-1.2179-0.2988-0.09780.36490.889-0.3221-0.00360.4884-0.16050.09420.4159-0.10280.6932-51.7411-46.16364.9273
101.568-0.0102-0.14381.29430.45191.8684-0.1764-0.3929-0.10520.22110.14290.07180.185-0.1054-0.00010.19050.05430.03230.27960.03640.1608-44.4684-32.825417.0344
111.9971-0.27080.27231.03830.76391.9141-0.0997-0.0818-0.3320.08910.05560.04820.3459-0.0786-0.00020.1880.00340.00780.19110.00330.1612-39.8371-36.36515.4616
121.53010.1979-0.19931.3280.27160.7594-0.0392-0.0218-0.2439-0.03450.0839-0.11420.22060.1827-00.20680.05720.01910.28960.01070.1646-29.9907-35.58554.022
130.01640.0189-0.00320.02780.01550.01880.0123-0.03030.37880.0895-0.1591-0.5551-0.320.537700.5463-0.1888-0.16320.6011-0.0290.6651-15.5984-3.98919.0733
141.2260.43050.51131.3354-0.61211.42470.01040.10670.33030.0727-0.0477-0.0261-0.30250.155800.2406-0.022-0.03890.24440.01350.2195-28.5822-11.1001-1.3217
151.5649-0.56771.19081.62120.12331.3438-0.06020.17810.28780.0308-0.0101-0.2245-0.28850.4004-0.00040.1995-0.0286-0.03010.3374-0.0190.176-22.4479-16.98218.4145
161.15570.43950.74390.9891-0.04780.5557-0.03840.0599-0.0323-0.00380.0015-0.19120.02050.1965-00.18070.0364-0.00130.3358-0.01110.1786-21.9632-27.05077.8359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 6:15)
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 8:14)
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)
9X-RAY DIFFRACTION9(chain C and resid 8:14)
10X-RAY DIFFRACTION10(chain C and resid 15:65)
11X-RAY DIFFRACTION11(chain C and resid 66:113)
12X-RAY DIFFRACTION12(chain C and resid 114:157)
13X-RAY DIFFRACTION13(chain D and resid 9:14)
14X-RAY DIFFRACTION14(chain D and resid 15:65)
15X-RAY DIFFRACTION15(chain D and resid 66:113)
16X-RAY DIFFRACTION16(chain D and resid 114:157)

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