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- PDB-5cft: Crystal Structure of ANT(2")-Ia in complex with AMPCPP and gentam... -

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Basic information

Entry
Database: PDB / ID: 5cft
TitleCrystal Structure of ANT(2")-Ia in complex with AMPCPP and gentamicin C1
ComponentsAminoglycoside Nucleotidyltransferase (2")-Ia
Keywordstransferase/antibiotic / antibiotic resistance / nucleotidyltransferase / AMPCPP / gentamicin / 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
gentamicin C1 / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / : / AadB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.5 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 1.4Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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: Aminoglycoside Nucleotidyltransferase (2")-Ia
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3406
Polymers20,9651
Non-polymers1,3755
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.580, 46.030, 89.000
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 Aminoglycoside Nucleotidyltransferase (2")-Ia / AadB


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 , 5 types, 236 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-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
#4: Chemical ChemComp-51G / gentamicin C1 / (1S,2S,3R,4S,6R)-4,6-diamino-3-({(2R,3R,6S)-3-amino-6-[(1R)-1-(methylamino)ethyl]tetrahydro-2H-pyran-2-yl}oxy)-2-hydrox ycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside


Mass: 477.595 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H43N5O7
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM MES, 30% PEG 200, 5% PEG 3000, 1mM MnCl2, 10 mM AMPCPP, 10mM gentamicin C1

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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: Mar 6, 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: 1.49→46.03 Å / Num. obs: 27966 / % possible obs: 99.7 % / Redundancy: 17.2 % / Biso Wilson estimate: 12.88 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.014 / Net I/σ(I): 31.1 / Num. measured all: 481527
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.49-1.534.80.4872.7952419680.26196.7
6.66-46.0330.80.028111.9116343780.00599.5

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Processing

Software
NameVersionClassification
PHENIXrefinement
StructureStudio2.2.1data collection
xia20.3.7.0data scaling
XSCALEdata scaling
XDSdata reduction
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: D_1000211507

Resolution: 1.5→31.993 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1741 1409 5.15 %Random selection
Rwork0.1473 25962 --
obs0.1487 27371 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.55 Å2 / Biso mean: 18.592 Å2 / Biso min: 6.1 Å2
Refinement stepCycle: final / Resolution: 1.5→31.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1379 0 85 231 1695
Biso mean--19.4 31.39 -
Num. residues----175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171632
X-RAY DIFFRACTIONf_angle_d1.7552253
X-RAY DIFFRACTIONf_chiral_restr0.071242
X-RAY DIFFRACTIONf_plane_restr0.01303
X-RAY DIFFRACTIONf_dihedral_angle_d12.704628
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.55360.27491380.20732497263599
1.5536-1.61580.18191410.160725602701100
1.6158-1.68940.17951450.144925552700100
1.6894-1.77840.17221350.135725842719100
1.7784-1.88980.17911390.134425452684100
1.8898-2.03570.16491330.126926042737100
2.0357-2.24060.14011420.127625852727100
2.2406-2.56460.15581440.131426252769100
2.5646-3.23070.19361370.146926402777100
3.2307-32.00070.17221550.16427672922100
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)
15.2421.61490.88613.18120.7072.89730.0106-0.22760.12440.1437-0.0690.2244-0.0615-0.04660.02160.11340.01340.02390.08660.02260.1085-15.3087-3.929923.0431
20.96050.2959-0.43061.1833-0.68941.4861-0.0243-0.0763-0.0401-0.0309-0.0091-0.0150.05670.10060.02910.07090.00230.00770.0774-0.00120.0731-9.228-1.754612.2289
33.01691.18370.4622.90910.70783.693-0.08820.5864-0.2796-0.48410.43680.27240.5679-0.1914-0.11310.2716-0.0952-0.09870.2380.05510.2075-18.1262-0.5416-5.0617
43.9965-0.6643-1.27361.1196-0.43231.3533-0.03310.2222-0.0292-0.13330.0249-0.01680.0139-0.134-0.00340.1062-0.01570.00920.11980.03330.1264-8.070510.1784-4.5519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 20 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 136 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 137 through 154 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 155 through 176 )A0

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