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- PDB-2zw6: Crystal structure of bleomycin N-acetyltransferase from bleomycin... -

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Basic information

Entry
Database: PDB / ID: 2zw6
TitleCrystal structure of bleomycin N-acetyltransferase from bleomycin-producing Streptomyces verticillus ATCC15003
ComponentsBleomycin acetyltransferase
KeywordsTRANSFERASE / dimer / two domains
Function / homology
Function and homology information


peptide-alanine-alpha-N-acetyltransferase activity / peptide-serine-alpha-N-acetyltransferase activity / cytoplasm
Similarity search - Function
Glyoxalase-like domain / Acetyltransferase (GNAT) domain / 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 / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. ...Glyoxalase-like domain / Acetyltransferase (GNAT) domain / 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 / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Bleomycin acetyltransferase
Similarity search - Component
Biological speciesStreptomyces verticillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOda, K. / Matoba, Y. / Sugiyama, M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Catalytic mechanism of bleomycin N-acetyltransferase proposed on the basis of its crystal structure.
Authors: Oda, K. / Matoba, Y. / Noda, M. / Kumagai, T. / Sugiyama, M.
History
DepositionDec 1, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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Assembly

Deposited unit
A: Bleomycin acetyltransferase
B: Bleomycin acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9276
Polymers64,5432
Non-polymers3844
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-85 kcal/mol
Surface area26760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.910, 100.910, 164.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Bleomycin acetyltransferase


Mass: 32271.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces verticillus (bacteria) / Strain: ATCC15003 / Gene: blmB / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: Q53796
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 108 / 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: 3.74 Å3/Da / Density % sol: 67.11 %
Crystal growTemperature: 293 K / Method: gel-tube counter diffusion / pH: 7.5
Details: 0.75% PEG 400, 1.0M ammonium sulfate, 0.1M Hepes , pH 7.5, gel-tube counter diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 27705 / Num. obs: 27705 / % possible obs: 81.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 11.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1915 / Rsym value: 0.271 / % possible all: 57.2

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZW4

2zw4


Resolution: 2.5→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1353 4.9 %RANDOM
Rwork0.211 ---
obs0.211 27662 81.1 %-
all-27662 --
Displacement parametersBiso mean: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4461 0 20 108 4589
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.61
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it5.011.5
X-RAY DIFFRACTIONx_mcangle_it7.492
X-RAY DIFFRACTIONx_scbond_it7.732
X-RAY DIFFRACTIONx_scangle_it10.62.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 151 4.7 %
Rwork0.315 3054 -
obs-3205 57.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep-2.paramtophcsdx-2.pro
X-RAY DIFFRACTION2so3.paramtoph19.sol
X-RAY DIFFRACTION3so3.top

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