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- PDB-2z3i: Crystal structure of blasticidin S deaminase (BSD) mutant E56Q co... -

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Basic information

Entry
Database: PDB / ID: 2z3i
TitleCrystal structure of blasticidin S deaminase (BSD) mutant E56Q complexed with substrate
ComponentsBlasticidin-S deaminase
KeywordsHYDROLASE / CYTIDINE DEAMINASE FAMILY / TETRAMER
Function / homology
Function and homology information


blasticidin-S deaminase / blasticidin-S deaminase activity / cytidine deaminase activity / response to antibiotic / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
: / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BLASTICIDIN S / CACODYLATE ION / Blasticidin-S deaminase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKumasaka, T. / Yamamoto, M. / Furuichi, M. / Nakasako, M. / Kimura, M. / Yamaguchi, I. / Ueki, T.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc
Authors: Kumasaka, T. / Yamamoto, M. / Furuichi, M. / Nakasako, M. / Teh, A.H. / Kimura, M. / Yamaguchi, I. / Ueki, T.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Blasticidin S Deaminase from Aspergillus Terreus
Authors: Nakasako, M. / Kimura, M. / Yamaguchi, I.
History
DepositionJun 4, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 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: Blasticidin-S deaminase
B: Blasticidin-S deaminase
C: Blasticidin-S deaminase
D: Blasticidin-S deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,40816
Polymers53,9094
Non-polymers2,49912
Water10,106561
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14120 Å2
ΔGint-137.5 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.330, 69.578, 145.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Blasticidin-S deaminase


Mass: 13477.261 Da / Num. of mol.: 4 / Mutation: E56Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Strain: S-712 / Plasmid: PET-12A / Production host: Escherichia coli (E. coli) / References: UniProt: P0C2P0, blasticidin-S deaminase
#2: Chemical
ChemComp-BLS / BLASTICIDIN S


Mass: 422.439 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H26N8O5 / Comment: antibiotic*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG8000, 0.1M SODIUM CACODYLATE, 50MM MAGNESIUM CHROLIDE, 1MM BLASTICIDIN-S, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationMonochromator: DIAMOND (400) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 48599 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.057

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WN5

1wn5


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.303 / SU ML: 0.074 / ESU R: 0.132 / ESU R Free: 0.129 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2436 5 %RANDOM
Rwork0.175 ---
obs0.178 46160 91.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.57 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å20 Å2
2---0.11 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3744 0 144 561 4449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223992
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5122.0075452
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5275520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13823.889144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68815592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8841528
X-RAY DIFFRACTIONr_chiral_restr0.0860.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023012
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.22155
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22845
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2436
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2670.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8791.52631
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52424136
X-RAY DIFFRACTIONr_scbond_it2.20631508
X-RAY DIFFRACTIONr_scangle_it3.284.51316
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 156 -
Rwork0.209 3150 -
obs--85.47 %

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