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- PDB-6mn3: Crystal structure of aminoglycoside acetyltransferase AAC(3)-IVa,... -

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Basic information

Entry
Database: PDB / ID: 6mn3
TitleCrystal structure of aminoglycoside acetyltransferase AAC(3)-IVa, apoenzyme
ComponentsAminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
KeywordsTRANSFERASE / ANTIBIOTIC_NAT FAMILY / ACETYLTRANSFERASE / AMINOGLYCOSIDE / ANTIBIOTIC RESISTANCE / COENZYME A / AAC(3)-IVA / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / National Institute of Allergy and Infectious Diseases / NIAID
Function / homologyaminoglycoside 3-N-acetyltransferase activity / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic / metal ion binding / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsStogios, P.J. / Evdokimova, E. / Wawrzak, Z. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Commun Biol / Year: 2022
Title: Structural and molecular rationale for the diversification of resistance mediated by the Antibiotic_NAT family.
Authors: Stogios, P.J. / Bordeleau, E. / Xu, Z. / Skarina, T. / Evdokimova, E. / Chou, S. / Diorio-Toth, L. / D'Souza, A.W. / Patel, S. / Dantas, G. / Wright, G.D. / Savchenko, A.
History
DepositionOct 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 6, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
B: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5218
Polymers56,2482
Non-polymers2736
Water4,450247
1
A: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2253
Polymers28,1241
Non-polymers1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2965
Polymers28,1241
Non-polymers1724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.170, 55.327, 94.342
Angle α, β, γ (deg.)90.00, 102.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Aminoglycoside N(3)-acetyltransferase, AAC(3)-IVa


Mass: 28124.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: aacC4, aac(3), aac(3)-IV, aac(3)IV, B9T59_28975, BEN53_26235, BJJ90_27515, BK373_27930, BK400_28640, BVL39_27730, BZL31_07055, BZL69_29365, C5P01_27985, C7235_00480, CR538_26885, CWS33_26775, ...Gene: aacC4, aac(3), aac(3)-IV, aac(3)IV, B9T59_28975, BEN53_26235, BJJ90_27515, BK373_27930, BK400_28640, BVL39_27730, BZL31_07055, BZL69_29365, C5P01_27985, C7235_00480, CR538_26885, CWS33_26775, CXB56_01995, DK267_24825, DK268_23980, DK278_24785, DK279_23955, DK288_24810, DK289_23980, pEC012_00026
Plasmid: pET19bTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold
References: UniProt: Q306W4, aminoglycoside 3-N-acetyltransferase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 0.1 M Tris pH 8.8, 0.2 M magnesium chloride, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 22593 / % possible obs: 99.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.08 / Net I/σ(I): 9.98
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.997 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 1154 / CC1/2: 0.524 / Rpim(I) all: 0.572 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(dev_3092: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SMA

3sma


Resolution: 2.4→29.769 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.76
RfactorNum. reflection% reflectionSelection details
Rfree0.2215 1123 5 %RANDOM
Rwork0.1762 ---
obs0.1785 22452 98.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3920 0 6 247 4173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034023
X-RAY DIFFRACTIONf_angle_d0.5795490
X-RAY DIFFRACTIONf_dihedral_angle_d17.4491486
X-RAY DIFFRACTIONf_chiral_restr0.042613
X-RAY DIFFRACTIONf_plane_restr0.005729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50920.32551400.2642661X-RAY DIFFRACTION100
2.5092-2.64140.30341410.24212694X-RAY DIFFRACTION100
2.6414-2.80680.27131400.22462631X-RAY DIFFRACTION99
2.8068-3.02330.26811400.21632672X-RAY DIFFRACTION99
3.0233-3.32720.24381370.19122621X-RAY DIFFRACTION98
3.3272-3.80780.20271380.15032607X-RAY DIFFRACTION97
3.8078-4.79420.16711400.1262666X-RAY DIFFRACTION98
4.7942-29.77090.18371470.15872777X-RAY DIFFRACTION100
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)
11.6181-0.38510.61774.1852-2.89016.18390.02670.0532-0.0657-0.5420.00090.04810.3932-0.0119-0.06130.21290.0025-0.02120.2233-0.04020.2194-43.1903-15.874671.1902
21.76521.59570.83863.5712-0.31982.4302-0.37560.6490.0487-1.69120.1859-0.35140.52720.09010.11920.9417-0.01980.10530.5289-0.00810.3366-36.9797-9.070353.5607
30.44110.7982-0.17881.5062-0.60580.1781-0.706-0.0242-1.4147-1.12610.3913-0.73310.92920.00880.44771.60310.13280.50211.11310.04690.9321-27.3348-8.40444.4418
40.59810.5078-0.14233.1234-1.12693.1989-0.0582-0.0146-0.0713-0.472-0.3563-0.9608-0.33150.89210.20960.3692-0.04260.09940.55190.11240.4887-25.4944-0.13864.9792
59.4243-3.2978-4.74646.47593.26743.19560.1509-0.59780.51730.2475-0.05030.0869-0.29870.2886-0.1740.31860.0063-0.08120.2108-0.0460.2507-6.416541.481998.1349
65.1265-0.0466-3.07611.9240.20386.4060.06390.10140.41030.0422-0.08180.0703-0.2813-0.32920.00530.16040.0104-0.05410.1583-0.00910.2552-8.769136.577289.0028
74.17040.78311.25835.20190.64283.30.10.2446-0.3361-0.2766-0.02790.30230.2605-0.251-0.0450.22040.0007-0.00990.2717-0.00720.2806-14.662927.227776.9184
81.8282-0.22580.72552.2828-0.07151.73460.24230.2988-0.2686-0.1537-0.17530.27110.1232-0.2043-0.06730.20140.0237-0.01570.2639-0.02380.3413-6.461318.088179.6077
96.3414-0.51492.43521.79432.56484.68840.05590.7537-0.8548-0.13730.22330.6837-0.55140.2813-0.33890.4433-0.1291-0.12430.39120.05540.7659-18.021911.238775.5871
101.2755-1.5681-0.77825.33013.25772.31720.0179-0.0683-0.0950.35290.0791-0.2130.2320.1788-0.12750.1621-0.0044-0.02590.23110.01950.27223.30920.954990.225
116.82333.4383-3.49965.89290.64349.0768-0.0817-0.2162-0.57280.50350.09480.411.1611-0.7941-0.06070.4273-0.0642-0.01510.38080.11010.5292-6.45682.532689.3453
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 61 )
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 172 )
3X-RAY DIFFRACTION3chain 'A' and (resid 173 through 190 )
4X-RAY DIFFRACTION4chain 'A' and (resid 191 through 257 )
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 17 )
6X-RAY DIFFRACTION6chain 'B' and (resid 18 through 52 )
7X-RAY DIFFRACTION7chain 'B' and (resid 53 through 128 )
8X-RAY DIFFRACTION8chain 'B' and (resid 129 through 174 )
9X-RAY DIFFRACTION9chain 'B' and (resid 175 through 190 )
10X-RAY DIFFRACTION10chain 'B' and (resid 191 through 234 )
11X-RAY DIFFRACTION11chain 'B' and (resid 235 through 257 )

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