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- PDB-5cfs: Crystal Structure of ANT(2")-Ia in complex with AMPCPP and tobramycin -

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Basic information

Entry
Database: PDB / ID: 5cfs
TitleCrystal Structure of ANT(2")-Ia in complex with AMPCPP and tobramycin
ComponentsAAD(2''),Gentamicin 2''-nucleotidyltransferase,Gentamicin resistance protein
Keywordstransferase/antibiotic / antibiotic resistance / nucleotidyltransferase / AMPCPP / 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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / : / TOBRAMYCIN / AadB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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: 2016
Title: Structural Analysis of the Tobramycin and Gentamicin Clinical Resistome Reveals Limitations for Next-generation Aminoglycoside Design.
Authors: Bassenden, A.V. / Rodionov, D. / Shi, K. / Berghuis, A.M.
History
DepositionJul 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AAD(2''),Gentamicin 2''-nucleotidyltransferase,Gentamicin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4507
Polymers20,9651
Non-polymers1,4856
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.720, 45.970, 89.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein AAD(2''),Gentamicin 2''-nucleotidyltransferase,Gentamicin resistance protein


Mass: 20964.518 Da / Num. of mol.: 1
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

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Non-polymers , 6 types, 181 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#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-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 100 mM MES pH 6.3, 28% PEG 200, 5% PEG 3000, 1mM MnCl2, 10 mM AMPCPP, 10mM tobramycin

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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: Feb 27, 2015 / 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: 1.7→37.1 Å / Num. obs: 19150 / % possible obs: 99.7 % / Redundancy: 25.6 % / Biso Wilson estimate: 17.82 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.011 / Net I/σ(I): 43.1 / Num. measured all: 489780
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.7-1.745.50.5742.6752913590.27499.9
7.6-37.138.10.026147.196362530.00599.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
StructureStudio2.2.1data collection
xia20.3.7.0data scaling
XDSdata reduction
XSCALEdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XJE

4xje


Resolution: 1.7→37.096 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1927 973 5.08 %
Rwork0.1661 18175 -
obs0.1674 19148 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.59 Å2 / Biso mean: 22.9559 Å2 / Biso min: 10.03 Å2
Refinement stepCycle: final / Resolution: 1.7→37.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1373 0 92 175 1640
Biso mean--28.13 35.47 -
Num. residues----176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061573
X-RAY DIFFRACTIONf_angle_d0.9782157
X-RAY DIFFRACTIONf_chiral_restr0.036234
X-RAY DIFFRACTIONf_plane_restr0.004285
X-RAY DIFFRACTIONf_dihedral_angle_d13.537602
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7001-1.78970.24381310.20125232654100
1.7897-1.90180.25761380.189625602698100
1.9018-2.04870.2391280.185825802708100
2.0487-2.25480.18471460.160925532699100
2.2548-2.5810.19111380.15362584272299
2.581-3.25150.16451370.161926272764100
3.2515-37.10470.18191550.160827482903100
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)
14.16630.64420.80432.8774-0.13853.0729-0.0531-0.18470.1951-0.0393-0.01230.270.1951-0.26750.0810.170.00120.01580.14430.01860.1464-18.1583-4.668221.8276
22.4045-0.08510.30991.66680.32512.29490.1113-0.3491-0.13440.09830.06270.0891-0.0012-0.0519-0.20740.1204-0.0160.01390.16980.01610.1306-14.58861.701215.996
31.1794-0.1362-0.48231.283-0.7642.0616-0.0246-0.0412-0.0046-0.08680.0313-0.02360.12920.1559-0.01310.1347-0.00210.01420.1253-0.00950.1416-9.331-2.13839.7661
44.3259-0.9161-1.75730.992-0.14651.23140.11010.3460.1357-0.1967-0.0243-0.026-0.0629-0.1233-0.09780.12980.00330.02970.15050.02060.1725-10.09519.8472-4.2337
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 16 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 41 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 152 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 153 through 176 )A0

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