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- PDB-6ctz: Structure of the GDP and kanamycin complex of APH(2")-IIia -

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Basic information

Entry
Database: PDB / ID: 6ctz
TitleStructure of the GDP and kanamycin complex of APH(2")-IIia
ComponentsGentamicin resistance protein
KeywordsTRANSFERASE/ANTIBIOTIC / aminoglycoside resistance / kinase / kanamycin / TRANSFERASE-ANTIBIOTIC complex
Function / homology
Function and homology information


Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / KANAMYCIN A / Gentamicin resistance protein
Similarity search - Component
Biological speciesEnterococcus gallinarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsSmith, C.A. / Vakulenko, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI057393 United States
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2019
Title: Structural basis for the diversity of the mechanism of nucleotide hydrolysis by the aminoglycoside-2''-phosphotransferases
Authors: Smith, C.A. / Toth, M. / Stewart, N.K. / Maltz, L. / Vakulenko, S.B.
History
DepositionMar 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.value / _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: Gentamicin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8137
Polymers33,7661
Non-polymers1,0476
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-50 kcal/mol
Surface area14020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.169, 58.982, 70.853
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Gentamicin resistance protein / aminoglycoside-2"-phosphotransferase-IIIa


Mass: 33766.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus gallinarum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P96762

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Non-polymers , 5 types, 375 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-KAN / KANAMYCIN A / Kanamycin A


Mass: 484.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36N4O11 / Comment: antibiotic*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.25 M magnesium chloride, 0.1 M Tris-HCl, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.34→39.086 Å / Num. obs: 73255 / % possible obs: 100 % / Redundancy: 14.3 % / Biso Wilson estimate: 14.7 Å2 / Net I/σ(I): 22.1
Reflection shellResolution: 1.34→1.36 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 2.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3TDW

3tdw


Resolution: 1.34→39.09 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 15.01
RfactorNum. reflection% reflection
Rfree0.171 3670 5.01 %
Rwork0.146 69585 -
obs0.147 73255 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 56 Å2 / Biso mean: 22.14 Å2 / Biso min: 8.19 Å2
Refinement stepCycle: final / Resolution: 1.34→39.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 66 380 2824
Biso mean--16.73 33.74 -
Num. residues----297
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.34-1.35760.25361400.196326312771
1.3576-1.37620.20761570.179726272784
1.3762-1.39590.19531300.161826632793
1.3959-1.41670.19211390.156526512790
1.4167-1.43890.22381390.147126302769
1.4389-1.46250.16191370.144526342771
1.4625-1.48770.1541410.136826552796
1.4877-1.51470.17981390.126326582797
1.5147-1.54390.20031410.136726692810
1.5439-1.57540.16381380.133226212759
1.5754-1.60960.17511390.128826582797
1.6096-1.64710.17911390.12426712810
1.6471-1.68830.14241390.122426422781
1.6883-1.73390.16621400.122326642804
1.7339-1.78490.15751410.125926682809
1.7849-1.84260.17011400.132426572797
1.8426-1.90840.16231410.129426862827
1.9084-1.98480.16881400.128126502790
1.9848-2.07510.1591410.13226832824
2.0751-2.18450.17381410.131826912832
2.1845-2.32140.14831420.136826862828
2.3214-2.50060.1811420.150127082850
2.5006-2.75220.15981420.155326952837
2.7522-3.15030.18561440.159827332877
3.1503-3.96840.16461450.149927582903
3.9684-39.10270.17411530.163228963049

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