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- PDB-4xje: CRYSTAL STRUCTURE OF ANT(2") IN COMPLEX WITH AMP AND TOBRAMYCIN -

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Basic information

Entry
Database: PDB / ID: 4xje
TitleCRYSTAL STRUCTURE OF ANT(2") IN COMPLEX WITH AMP AND TOBRAMYCIN
ComponentsAadB
Keywordstransferase/antibiotic / antibiotic resistance / nucleotidyltransferase / tobramycin / Rossmann fold / transferase-antibiotic complex
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
Aminoglycoside-2''-adenylyltransferase / Aminoglycoside-2''-adenylyltransferase / Beta Polymerase; domain 2 - #40 / Beta Polymerase; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / TOBRAMYCIN / AadB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.88 Å
AuthorsRodionov, D. / Bassenden, A.V. / Berghuis, A.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)CIHR MOP-13107 Canada
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Revisiting the Catalytic Cycle and Kinetic Mechanism of AminoglycosideO-Nucleotidyltransferase(2′′): A Structural and Kinetic Study.
Authors: Bassenden, A.V. / Park, J. / Rodionov, D. / Berghuis, A.M.
History
DepositionJan 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _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: AadB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8714
Polymers20,9651
Non-polymers9073
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.020, 42.020, 191.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Detailsbiological unit is the same as asym.

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Components

#1: Protein AadB


Mass: 20964.518 Da / Num. of mol.: 1 / Fragment: unp residues 73-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: aadB, TNCP6 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6X3H6
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-TOY / TOBRAMYCIN / 4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL


Mass: 467.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37N5O9 / Comment: antibiotic*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.13 Å3/Da / Density % sol: 42.25 % / Description: 0.2 mm X 0.1 mm diamond-shaped
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.04 M potassium di-hydrogen phosphate, 16% PEG 8000, 20% glycerol

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 11, 2014 / Details: 2x2 binning
RadiationMonochromator: Rigaku VariMax-HF focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.88→47.99 Å / Num. obs: 14841 / % possible obs: 99.5 % / Redundancy: 31.7 % / Biso Wilson estimate: 18.383 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.01 / Net I/σ(I): 53.5 / Num. measured all: 469871
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.88-1.9313.30.51151370210320.13997.1
8.41-47.9934.50.018184.773392130.00399.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.9-1692refinement
StructureStudio2.2.1data collection
xia20.3.7.0data reduction
SHELX2013phasing
PDB_EXTRACT3.15data extraction
XDSdata scaling
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.88→47.99 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1884 789 5.32 %Random selection
Rwork0.1672 14050 --
obs0.1684 14839 99.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.93 Å2 / Biso mean: 25.8225 Å2 / Biso min: 10.53 Å2
Refinement stepCycle: final / Resolution: 1.88→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1384 0 61 162 1607
Biso mean--19.28 32.91 -
Num. residues----175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031503
X-RAY DIFFRACTIONf_angle_d0.8752057
X-RAY DIFFRACTIONf_chiral_restr0.031227
X-RAY DIFFRACTIONf_plane_restr0.003273
X-RAY DIFFRACTIONf_dihedral_angle_d12.691565
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8801-1.99790.21461290.22862243237297
1.9979-2.15210.19651240.17632243236799
2.1521-2.36870.21371290.18132304243399
2.3687-2.71140.20751130.165823522465100
2.7114-3.4160.17851390.161523602499100
3.416-48.01060.17431550.154125482703100
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)
10.0310.016-0.01840.00980.0050.02990.12990.15640.22450.01790.06790.28770.1334-0.21160.00190.2216-0.0444-0.05490.24990.03410.2512-5.825825.875451.0171
20.104-0.04830.00820.02660.03450.1745-0.06870.02190.0795-0.0850.14690.12090.007-0.0350.00020.1529-0.0348-0.00920.12960.01450.16681.386426.056158.5638
30.5619-0.15780.0490.1247-0.08890.0594-0.10070.1657-0.0764-0.22160.1099-0.04350.3045-0.07730.04060.2367-0.0619-0.01860.16810.00260.12971.934714.281150.917
40.3034-0.09010.18770.08380.04040.33010.0552-0.0912-0.1775-0.02890.067-0.02960.2902-0.21020.01910.1436-0.04460.02590.10890.02060.17032.032714.622866.2594
50.0132-0.05430.04050.3545-0.16050.2616-0.00870.07090.0084-0.0924-0.0687-0.02440.04230.0263-0.0070.13310.01680.00450.1259-0.00110.149410.442223.045562.88
60.0024-0.0073-0.01680.00560.01660.0344-0.0009-0.0560.2625-0.0256-0.03140.16150.07180.0953-00.1622-0.01310.01610.13820.00510.159213.113230.080766.3884
70.2562-0.1185-0.08850.36370.60821.07210.08220.07350.17060.15120.0251-0.10150.25840.30050.02550.21910.0298-0.00720.11840.00520.159617.572215.790572.1296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 18 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 44 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 99 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 100 through 112 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 145 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 146 through 160 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 161 through 176 )A0

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