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- PDB-1jie: Crystal structure of bleomycin-binding protein from bleomycin-pro... -

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Basic information

Entry
Database: PDB / ID: 1jie
TitleCrystal structure of bleomycin-binding protein from bleomycin-producing Streptomyces verticillus complexed with metal-free bleomycin
Componentsbleomycin-binding protein
KeywordsPROTEIN BINDING / protein-ligand complex
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 / 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 A2 / Bleomycin resistance protein
Similarity search - Component
Biological speciesStreptomyces verticillus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSugiyama, M. / Kumagai, T. / Hayashida, M. / Maruyama, M. / Matoba, Y.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: The 1.6-A crystal structure of the copper(II)-bound bleomycin complexed with the bleomycin-binding protein from bleomycin-producing Streptomyces verticillus.
Authors: Sugiyama, M. / Kumagai, T. / Hayashida, M. / Maruyama, M. / Matoba, Y.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: The 1.5 A crystal structure of a bleomycin resistance determinant from bleomycin-producing Streptomyces verticillus
Authors: Kawano, Y. / Kumagai, T. / Muta, K. / Matoba, Y. / Davies, J. / Sugiyama, M.
#2: 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.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and preliminary X-ray diffraction studies of bleomycin-binding protein from bleomycin-producing Streptomyces verticillus
Authors: Kumagai, T. / Muta, K. / Matoba, Y. / Kawano, Y. / Kamiya, N. / Davies, J. / Sugiyama, M.
History
DepositionJul 2, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: bleomycin-binding protein
B: bleomycin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3204
Polymers26,4872
Non-polymers2,8332
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-46 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.520, 83.420, 43.240
Angle α, β, γ (deg.)90.00, 104.88, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a homodimer.

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Components

#1: Protein bleomycin-binding protein


Mass: 13243.607 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces verticillus (bacteria) / Gene: blmA / Plasmid: pKKtrp / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q53793
#2: Chemical ChemComp-BLM / BLEOMYCIN A2 / N1-[3-(DIMETHYLSULFONIO)-PROPYL]BLEOMYCINAMIDE


Mass: 1416.560 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H85N17O21S3 / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 1.94 Å3/Da / Density % sol: 36.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG4000, ammonium acetate, sodium cacodylate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
117.5 %(w/v)PEG40001reservoir
20.2 Mammonium acetate1reservoir
30.1 Msodium cacodylate1reservoirpH5.6
410 mMsodium phosphate1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 1, 1999
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. obs: 19023 / % possible obs: 80.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.48 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.4
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 2.25 / % possible all: 55.1
Reflection
*PLUS
Lowest resolution: 100 Å
Reflection shell
*PLUS
% possible obs: 55.1 %

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QTO

1qto


Resolution: 1.8→10 Å / Num. parameters: 8949 / Num. restraintsaints: 8738 / Cross valid method: FREE R / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1862 10 %RANDOM
all0.156 17018 --
obs0.16 17018 75.9 %-
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2199
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 192 139 2229
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.022
X-RAY DIFFRACTIONs_zero_chiral_vol0.05
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.04
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.161 / Rfactor Rfree: 0.219 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_plane_restr0.022
X-RAY DIFFRACTIONs_chiral_restr0.05

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