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- PDB-6p08: Ternary structure of the E52D mutant of ANT-4'' with Neomycin, AM... -

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Basic information

Entry
Database: PDB / ID: 6p08
TitleTernary structure of the E52D mutant of ANT-4'' with Neomycin, AMP and Pyrophosphate
ComponentsKanamycin nucleotidyltransferase
KeywordsTRANSFERASE/ANTIBIOTIC / Aminoglycoside nucelotidyl transferase (ANT) / Aminoglycoside modifying enzymes (AGMEs) / DNA polymerase / ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC complex
Function / homology
Function and homology information


nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / response to antibiotic
Similarity search - Function
Kanamycin nucleotidyltransferase, C-terminal / KNTase C-terminal domain / Nucleotidyltransferases domain 2 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / NEOMYCIN / PYROPHOSPHATE / Aminoglycoside nucleotidyltransferase (4')
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsSelvaraj, B. / Cuneo, M.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
Department of Energy (DOE, United States) United States
CitationJournal: Acs Catalysis / Year: 2020
Title: "Catch and Release": a Variation of the Archetypal Nucleotidyl Transfer Reaction
Authors: Selvaraj, B. / Kocaman, S. / Trifas, M. / Serpersu, E.H. / Cuneo, M.J.
History
DepositionMay 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation
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.year
Revision 1.2May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 11, 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 / struct_conn_type
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_asym_id / _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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kanamycin nucleotidyltransferase
D: Kanamycin nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,62112
Polymers58,2442
Non-polymers2,37710
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10310 Å2
ΔGint-83 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.750, 99.300, 101.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Kanamycin nucleotidyltransferase


Mass: 29121.855 Da / Num. of mol.: 2 / Mutation: E52D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Gene: knt, kan
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P05058, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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Non-polymers , 5 types, 238 molecules

#2: Chemical ChemComp-NMY / NEOMYCIN / MYCIFRADIN / NEOMAS / PIMAVECORT / VONAMYCIN


Mass: 614.644 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H46N6O13 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / Details: 18% PEG 8K, 0.1 M Tris pH 8.0, 0.1 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.27→49.65 Å / Num. obs: 30558 / % possible obs: 97.6 % / Redundancy: 6.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.05 / Rrim(I) all: 0.134 / Net I/σ(I): 8.8
Reflection shellResolution: 2.27→2.3 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2512 / CC1/2: 0.919 / Rpim(I) all: 0.243 / Rrim(I) all: 0.476 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KNY

1kny


Resolution: 2.27→49.65 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.39
RfactorNum. reflection% reflection
Rfree0.2246 1424 5.08 %
Rwork0.1944 --
obs0.196 30482 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.27→49.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4036 0 150 228 4414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064316
X-RAY DIFFRACTIONf_angle_d0.9935874
X-RAY DIFFRACTIONf_dihedral_angle_d8.843430
X-RAY DIFFRACTIONf_chiral_restr0.079658
X-RAY DIFFRACTIONf_plane_restr0.005728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.27110.28991280.24022496X-RAY DIFFRACTION94
2.2711-2.35220.27351320.23312532X-RAY DIFFRACTION96
2.3522-2.44640.26681400.22772548X-RAY DIFFRACTION96
2.4464-2.55770.27361320.22132540X-RAY DIFFRACTION95
2.5577-2.69260.28121280.21742594X-RAY DIFFRACTION96
2.6926-2.86130.2311300.22812607X-RAY DIFFRACTION97
2.8613-3.08220.27971630.2222654X-RAY DIFFRACTION99
3.0822-3.39230.24961130.20332693X-RAY DIFFRACTION99
3.3923-3.8830.20911690.17972689X-RAY DIFFRACTION100
3.883-4.89150.1651630.15492724X-RAY DIFFRACTION99
4.8915-49.66260.1841510.16322856X-RAY DIFFRACTION99

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