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- PDB-2z3h: Crystal structure of blasticidin S deaminase (BSD) complexed with... -

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Basic information

Entry
Database: PDB / ID: 2z3h
TitleCrystal structure of blasticidin S deaminase (BSD) complexed with deaminohydroxy blasticidin S
ComponentsBlasticidin-S deaminase
KeywordsHYDROLASE / CYTIDINE DEAMINASE FAMILY / ZINC / 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 / cytosol
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
Chem-BLO / Blasticidin-S deaminase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: 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_conn / 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_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

Downloads & links

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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)55,86812
Polymers53,9134
Non-polymers1,9558
Water12,286682
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-87 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.300, 69.275, 146.535
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: 13478.245 Da / Num. of mol.: 4
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-BLO / 1-(4-{[(3R)-3-AMINO-5-{[(Z)-AMINO(IMINO)METHYL](METHYL)AMINO}PENTANOYL]AMINO}-2,3,4-TRIDEOXY-D-ERYTHRO-HEX-2-ENOPYRANURONOSYL)-4-HYDROXYPYRIMIDIN-2(1H)-ONE / DEAMINOHYDROXY BLASTICIDIN-S


Mass: 423.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H25N7O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 682 / 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: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG8000, 0.1M SODIUM CACODYLATE, 50MM MAGNESIUM CHLORIDE, 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: 1.5→50 Å / Num. obs: 89147 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.091

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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: 1.5→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.985 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.065 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.185 4460 5 %RANDOM
Rwork0.172 ---
obs0.173 84565 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2---0.43 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3703 0 124 686 4513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223894
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2292.0115332
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0665521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72623.714140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76215600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6511531
X-RAY DIFFRACTIONr_chiral_restr0.0690.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022977
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.22139
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22848
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2540
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.611.52587
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05824100
X-RAY DIFFRACTIONr_scbond_it1.64631420
X-RAY DIFFRACTIONr_scangle_it2.7134.51232
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 314 -
Rwork0.2 6090 -
obs--98.28 %

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