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- PDB-1ecs: THE 1.7 A CRYSTAL STRUCTURE OF A BLEOMYCIN RESISTANCE DETERMINANT... -

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Basic information

Entry
Database: PDB / ID: 1ecs
TitleTHE 1.7 A CRYSTAL STRUCTURE OF A BLEOMYCIN RESISTANCE DETERMINANT ENCODED ON THE TRANSPOSON TN5
ComponentsBLEOMYCIN RESISTANCE PROTEIN
KeywordsANTIBIOTIC INHIBITOR / ARM-EXCHANGE
Function / homology
Function and homology information


response to antibiotic
Similarity search - Function
Bleomycin resistance protein / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
Bleomycin resistance protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMaruyama, M. / Matoba, Y. / Kumagai, T. / Sugiyama, M.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Crystal structures of the transposon Tn5-carried bleomycin resistance determinant uncomplexed and complexed with bleomycin.
Authors: Maruyama, M. / Kumagai, T. / Matoba, Y. / Hayashida, M. / Fujii, T. / Hata, Y. / Sugiyama, M.
#1: Journal: FEBS Lett. / Year: 1999
Title: Characterizaton of the bleomycin resistance determinant encoded on the transposon Tn5
Authors: Kumagai, T. / Nakano, T. / Maruyama, M. / Mochizuki, H. / Sugiyama, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and preliminary X-ray diffraction studies of bleomycin-binding protein encoded on the transposon Tn5
Authors: Kumagai, T. / Maruyama, M. / Matoba, Y. / Kawano, Y. / Sugiyama, M.
History
DepositionJan 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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_ref_seq_dif / struct_site
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.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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BLEOMYCIN RESISTANCE PROTEIN
B: BLEOMYCIN RESISTANCE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4545
Polymers28,0262
Non-polymers4293
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint3 kcal/mol
Surface area10780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.330, 85.030, 78.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-486-

HOH

21A-500-

HOH

31B-512-

HOH

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Components

#1: Protein BLEOMYCIN RESISTANCE PROTEIN


Mass: 14012.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: TRANSPOSON TN5 / Plasmid: PKKTRP / Production host: Escherichia coli (E. coli) / References: UniProt: P13081
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 6000, calcium acetate, sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal
*PLUS
Density % sol: 49 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 %PEG60001reservoir
20.1 Mcalcium acetate1reservoir
30.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Feb 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→58.77 Å / Num. obs: 28095 / % possible obs: 92.4 % / Observed criterion σ(I): 1 / Redundancy: 10.5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 6.1
Reflection shellResolution: 1.7→1.77 Å / Redundancy: 3.46 % / Rmerge(I) obs: 0.253 / % possible all: 78.1
Reflection
*PLUS
Num. measured all: 295760
Reflection shell
*PLUS
% possible obs: 78.1 %

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
WEISdata reduction
WEISdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DIMERIC BLMA (1QTO)

1qto


Resolution: 1.7→5 Å / Num. parameters: 8115 / Num. restraintsaints: 7896 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
obs0.191 -90.7 %
all-26798 -
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2028.5
Refinement stepCycle: LAST / Resolution: 1.7→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 27 111 2028
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.026
X-RAY DIFFRACTIONs_zero_chiral_vol0.036
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.046
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.044
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg1.23

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