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- PDB-1byl: BLEOMYCIN RESISTANCE PROTEIN FROM STREPTOALLOTEICHUS HINDUSTANUS -

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Basic information

Entry
Database: PDB / ID: 1byl
TitleBLEOMYCIN RESISTANCE PROTEIN FROM STREPTOALLOTEICHUS HINDUSTANUS
ComponentsPROTEIN (BLEOMYCIN RESISTANCE PROTEIN)
KeywordsANTIBIOTIC / ANTIBIOTIC RESISTANCE / BLEOMYCIN / DRUG SEQUESTERING / CHAIN SWAPPING
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 resistance protein
Similarity search - Component
Biological speciesStreptoalloteichus hindustanus (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.3 Å
AuthorsDumas, P. / Bergdoll, M. / Cagnon, C. / Masson, J.M.
Citation
Journal: EMBO J. / Year: 1994
Title: Crystal structure and site-directed mutagenesis of a bleomycin resistance protein and their significance for drug sequestering.
Authors: Dumas, P. / Bergdoll, M. / Cagnon, C. / Masson, J.M.
#1: Journal: Embo J. / Year: 1989
Title: Crystallization and Preliminary X-Ray Data of a Phleomycin-Binding Protein from Streptoalloteichus Hindistanus
Authors: Rondeau, J.M. / Cagnon, C. / Moras, D. / Masson, J.M.
#2: Journal: FEBS Lett. / Year: 1988
Title: Bleomycin Resistance Conferred by a Drug-Binding Protein
Authors: Gatignol, A. / Durand, H. / Tiraby, G.
#3: Journal: Protein Sci. / Year: 1998
Title: All in the Family: Structural and Evolutionary Relationships Among Three Modular Proteins with Functions and Variable Assembly
Authors: Bergdoll, M. / Eltis, L.D. / Cameron, A.D. / Dumas, P. / Bolin, J.T.
History
DepositionOct 17, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 21, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (BLEOMYCIN RESISTANCE PROTEIN)


Theoretical massNumber of molelcules
Total (without water)13,9531
Polymers13,9531
Non-polymers00
Water1,11762
1
A: PROTEIN (BLEOMYCIN RESISTANCE PROTEIN)

A: PROTEIN (BLEOMYCIN RESISTANCE PROTEIN)


Theoretical massNumber of molelcules
Total (without water)27,9072
Polymers27,9072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3510 Å2
ΔGint-30 kcal/mol
Surface area11340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)48.400, 48.400, 111.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTHE PROTEIN'S COORDINATES IN THIS FILE CORRESPOND TO HALF OF THE FUNCTIONNAL UNIT THE ACTIVE MOLECULE IS MADE UP OF TWO TIGHTLY INTERACTING MONOMERS WHICH ARE INVOLVED IN MUTUAL ARM EXCHANGE.

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Components

#1: Protein PROTEIN (BLEOMYCIN RESISTANCE PROTEIN) / SH-BLE


Mass: 13953.388 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptoalloteichus hindustanus (bacteria)
Description: DROCOURT, D., CALMELS, T., REYNES, J.P., BARON, M. & TIRABY, G. (1990) NUCLEIC ACIDS RES., 18, 4009.
Cellular location: CYTOPLASMICCytoplasm / Gene: SH BLE / Plasmid: PIN-III-OMPA2 / Cellular location (production host): PERIPLASM / Gene (production host): SH BLE / Production host: Escherichia coli (E. coli) / Strain (production host): SG936 / References: UniProt: P17493
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHREE EXTRA RESIDUES (ALA -2, GLU -1 & PHE 0) ARE PRESENT AT THE N-TERMINUS AND ARE PART OF AN ...THREE EXTRA RESIDUES (ALA -2, GLU -1 & PHE 0) ARE PRESENT AT THE N-TERMINUS AND ARE PART OF AN INCOMPLETELY CLEAVED EXPRESSION TAG AT THE C-TERMINUS END, THE LAST RESIDUES GLU122, GLN123, AND ASP124 ARE NOT VISIBLE IN THE DENSITY MAP

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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: 2.3 Å3/Da / Density % sol: 50 %
Description: LOCHVAT IS A SCALING AND HEAVY ATOM SITE DETERMINATION PROGRAM BY P. DUMAS [ ACTA CRYST A50 (1994) 526-546]
Crystal growpH: 6 / Details: SEE REFERENCE 2, pH 6.0
Crystal grow
*PLUS
Method: other / Details: Rondeau, J.M., (1989) J. Mol. Biol., 207, 645.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 15, 1991
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→44.5 Å / Num. obs: 5959 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 8.3 % / Rsym value: 0.669 / Net I/σ(I): 48.4
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4.24 / Rsym value: 0.204 / % possible all: 58
Reflection
*PLUS
Num. measured all: 49546 / Rmerge(I) obs: 0.067

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Processing

Software
NameVersionClassification
LOCHVAT(SEEREMARK)model building
CCP4model building
PHASERphasing
X-PLOR2.1refinement
X-GENdata reduction
X-GENdata scaling
LOCHVAT(SEE REMARK)phasing
CCP4(REFINEphasing
PHARE)phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001
Cross valid method: ANOMALOUS DIFFERENCE OF THE NATIVE DATA SET ALLOWING TO LOCATE ALL SULFUR ATOMS
σ(F): 2
RfactorNum. reflection% reflection
Rwork0.176 --
obs0.176 5724 93 %
Displacement parametersBiso mean: 17.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms959 0 0 62 1021
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.38 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.283 120 -
obs--21 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 2.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.9 Å2
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 3.2
LS refinement shell
*PLUS
% reflection Rfree: 21 % / Rfactor Rwork: 0.283

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