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

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Basic information

Entry
Database: PDB / ID: 1jif
TitleCrystal structure of bleomycin-binding protein from bleomycin-producing Streptomyces verticillus complexed with copper(II)-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 / COPPER (II) ION / Bleomycin resistance protein
Similarity search - Component
Biological speciesStreptomyces verticillus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.value / _struct_conn.pdbx_dist_value / _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.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_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-binding protein
B: bleomycin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5188
Polymers26,4872
Non-polymers3,0316
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-97 kcal/mol
Surface area11380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.730, 83.470, 43.060
Angle α, β, γ (deg.)90.00, 106.20, 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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 1.92 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG4000, ammonium acetate, sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130.0 %(w/v)PEG40001reservoir
20.2 Mammonium acetate1reservoir
30.1 Msodium cacodylate1reservoirpH6.0

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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: Apr 1, 2000
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. obs: 30741 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.29 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.4
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 1.98 / % possible all: 84.5
Reflection
*PLUS
Lowest resolution: 100 Å

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→10 Å / Num. parameters: 9018 / Num. restraintsaints: 8881 / Cross valid method: FREE R / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 2928 11 %RANDOM
all0.15 26405 --
obs0.158 -83.3 %-
Refine analyzeNum. disordered residues: 13 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2180
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 216 117 2243
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_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.07
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0.06
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor all: 0.15 / Rfactor obs: 0.159 / Rfactor Rfree: 0.208 / Rfactor Rwork: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.038
X-RAY DIFFRACTIONs_plane_restr0.027
X-RAY DIFFRACTIONs_chiral_restr0.07

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