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- PDB-1xrk: Crystal structure of a mutant bleomycin binding protein from Stre... -

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Basic information

Entry
Database: PDB / ID: 1xrk
TitleCrystal structure of a mutant bleomycin binding protein from Streptoalloteichus hindustanus displaying increased thermostability
ComponentsBleomycin resistance protein
KeywordsANTIBIOTIC INHIBITOR / Arm exchange / Ligand binding protein / Thermostable mutant
Function / homology
Function and homology information


response to antibiotic
Similarity search - Function
Glyoxalase superfamily protein / 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 speciesStreptoalloteichus hindustanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBrouns, S.J.J. / Wu, H. / Akerboom, J. / Turnbull, A.P. / de Vos, W.M. / Van der Oost, J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Engineering a selectable marker for hyperthermophiles
Authors: Brouns, S.J.J. / Wu, H. / Akerboom, J. / Turnbull, A.P. / de Vos, W.M. / van der Oost, J.
History
DepositionOct 15, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)30,9607
Polymers27,8392
Non-polymers3,1215
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-71 kcal/mol
Surface area10750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.983, 66.617, 47.179
Angle α, β, γ (deg.)90.00, 117.43, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains a biological dimer.

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Components

#1: Protein Bleomycin resistance protein / Bleomycin binding protein / BRP / Phleomycin resistance protein


Mass: 13919.370 Da / Num. of mol.: 2 / Mutation: G18E, D32V, L63Q, G98V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptoalloteichus hindustanus (bacteria)
Gene: shble / Plasmid: pET26b, pRIL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17493
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.2 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: ammonium sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9083 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 3, 2003 / Details: Mirrors
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9083 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 87740 / Num. obs: 36444 / % possible obs: 94.4 % / Rsym value: 0.043 / Net I/σ(I): 20.3
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 3.9 / Num. unique all: 1714 / Rsym value: 0.189 / % possible all: 88.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JIE

1jie


Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.586 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19425 1840 5.1 %RANDOM
Rwork0.17403 ---
obs0.17508 34580 94.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.23 Å2
2--0.45 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 197 288 2368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222135
X-RAY DIFFRACTIONr_bond_other_d0.0020.021830
X-RAY DIFFRACTIONr_angle_refined_deg1.6642.022937
X-RAY DIFFRACTIONr_angle_other_deg1.43234211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0355239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23724.02197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06515273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9841514
X-RAY DIFFRACTIONr_chiral_restr0.0990.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022337
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02445
X-RAY DIFFRACTIONr_nbd_refined0.1920.2404
X-RAY DIFFRACTIONr_nbd_other0.2020.21888
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21060
X-RAY DIFFRACTIONr_nbtor_other0.0870.21178
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2189
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.226
X-RAY DIFFRACTIONr_mcbond_it0.9361.51240
X-RAY DIFFRACTIONr_mcbond_other0.191.5494
X-RAY DIFFRACTIONr_mcangle_it1.32821943
X-RAY DIFFRACTIONr_scbond_it1.93331129
X-RAY DIFFRACTIONr_scangle_it2.8184.5994
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 116 -
Rwork0.196 2384 -
obs--87.69 %

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