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- PDB-1kan: MOLECULAR STRUCTURE OF KANAMYCIN NUCLEOTIDYLTRANSFERASE DETERMINE... -

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Basic information

Entry
Database: PDB / ID: 1kan
TitleMOLECULAR STRUCTURE OF KANAMYCIN NUCLEOTIDYLTRANSFERASE DETERMINED TO 3.0-ANGSTROMS RESOLUTION
ComponentsKANAMYCIN NUCLEOTIDYLTRANSFERASE
KeywordsNUCLEOTIDYLTRANSFERASE
Function / homologyKanamycin nucleotidyltransferase, C-terminal / KNTase C-terminal domain / nucleotidyltransferase activity / Nucleotidyltransferase superfamily / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / response to antibiotic / Kanamycin nucleotidyltransferase
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsHolden, H.M. / Rayment, I. / Sakon, J.
CitationJournal: Biochemistry / Year: 1993
Title: Molecular structure of kanamycin nucleotidyltransferase determined to 3.0-A resolution.
Authors: Sakon, J. / Liao, H.H. / Kanikula, A.M. / Benning, M.M. / Rayment, I. / Holden, H.M.
History
DepositionAug 13, 1993Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KANAMYCIN NUCLEOTIDYLTRANSFERASE
B: KANAMYCIN NUCLEOTIDYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)57,8032
Polymers57,8032
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.900, 78.900, 219.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein KANAMYCIN NUCLEOTIDYLTRANSFERASE / / Coordinate model: Cα atoms only


Mass: 28901.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
References: UniProt: P05057, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.31 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 %PEG80001drop
2100 mM1dropKCl
325 mMHEPES1drop
43 mM1dropCoCl2
52.5 mM1dropNaN3
615.0 %PEG80001reservoir
750 mMHEPES1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 9999 Å / Num. obs: 13914 / % possible obs: 95 % / Num. measured all: 70244 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.21 Å / % possible obs: 2243 % / Num. possible: 96 / Num. unique obs: 3586 / Rmerge(I) obs: 0.209

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.189 / Highest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms506 0 0 0 506
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg3
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_improper_angle_d0.009

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