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- PDB-2de3: Crystal structure of DSZB C27S mutant in complex with 2'-hydroxyb... -

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Basic information

Entry
Database: PDB / ID: 2de3
TitleCrystal structure of DSZB C27S mutant in complex with 2'-hydroxybiphenyl-2-sulfinic acid
ComponentsDIBENZOTHIOPHENE DESULFURIZATION ENZYME B
KeywordsHYDROLASE / ALPHA-BETA
Function / homology
Function and homology information


2'-hydroxybiphenyl-2-sulfinate desulfinase / 2'-hydroxybiphenyl-2-sulfinate desulfinase activity / dibenzothiophene catabolic process / monooxygenase activity / cytoplasm
Similarity search - Function
D-Maltodextrin-Binding Protein; domain 2 - #270 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 2'-HYDROXY-1,1'-BIPHENYL-2-SULFINIC ACID / 2'-hydroxybiphenyl-2-sulfinate desulfinase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLee, W.C. / Ohshiro, T. / Matsubara, T. / Izumi, Y. / Tanokura, M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal structure and desulfurization mechanism of 2'-hydroxybiphenyl-2-sulfinic acid desulfinase.
Authors: Lee, W.C. / Ohshiro, T. / Matsubara, T. / Izumi, Y. / Tanokura, M.
History
DepositionFeb 8, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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: DIBENZOTHIOPHENE DESULFURIZATION ENZYME B
B: DIBENZOTHIOPHENE DESULFURIZATION ENZYME B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7367
Polymers78,1252
Non-polymers6115
Water10,395577
1
A: DIBENZOTHIOPHENE DESULFURIZATION ENZYME B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3563
Polymers39,0621
Non-polymers2932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DIBENZOTHIOPHENE DESULFURIZATION ENZYME B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3804
Polymers39,0621
Non-polymers3183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.670, 46.190, 113.960
Angle α, β, γ (deg.)90.00, 115.81, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1001-

MG

21B-2529-

HOH

31B-2553-

HOH

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Components

#1: Protein DIBENZOTHIOPHENE DESULFURIZATION ENZYME B


Mass: 39062.496 Da / Num. of mol.: 2 / Mutation: C27S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: IGTS8 / Gene: DSZB / Production host: Escherichia coli (E. coli)
References: UniProt: P54997, 2'-hydroxybiphenyl-2-sulfinate desulfinase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-OBP / 2'-HYDROXY-1,1'-BIPHENYL-2-SULFINIC ACID / 2'-HYDROXYBIPHENYL-2-SULFINIC ACID


Mass: 234.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10O3S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 577 / 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: 2.3 Å3/Da / Density % sol: 47.2 %
Crystal growpH: 7
Details: PEG 6000, PEG 8000, HEPES, MAGNESIUM ACETATE, PH 7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K, pH 7.00

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.6→54.23 Å / Num. obs: 354446 / % possible obs: 100 % / Biso Wilson estimate: 14.25 Å2
Reflection shellResolution: 1.6→1.69 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→54.23 Å
RfactorNum. reflectionSelection details
Rfree0.196 4816 RANDOM
Rwork0.18 --
obs0.18 96079 -
Displacement parametersBiso mean: 14.481 Å2
Refinement stepCycle: LAST / Resolution: 1.6→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5225 0 41 577 5843
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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