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- PDB-2dd4: Thiocyanate hydrolase (SCNase) from Thiobacillus thioparus recomb... -

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Basic information

Entry
Database: PDB / ID: 2dd4
TitleThiocyanate hydrolase (SCNase) from Thiobacillus thioparus recombinant apo-enzyme
Components(Thiocyanate hydrolase ...) x 3
KeywordsHYDROLASE / cobalt / metalloprotein / sulfenic acid / sulfinic acid / nitrile hydratase / thiocyanate / carbonyl sulfide / claw setting / protein / enzyme / complex / model complex / non-corrin
Function / homology
Function and homology information


thiocyanate hydrolase / thiocyanate hydrolase activity / thiocyanate catabolic process / : / transition metal ion binding
Similarity search - Function
Thiocyanate hydrolase, gamma subunit / Nitrile hydratase, beta subunit / Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase beta subunit domain / Nitrile hydratase beta subunit, N-terminal / : / Nitrile hydratase beta subunit, C-terminal / Nitrile hydratase beta subunit, N-terminal / Nitrile hydratase alpha subunit /Thiocyanate hydrolase gamma subunit ...Thiocyanate hydrolase, gamma subunit / Nitrile hydratase, beta subunit / Nitrile Hydratase; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase beta subunit domain / Nitrile hydratase beta subunit, N-terminal / : / Nitrile hydratase beta subunit, C-terminal / Nitrile hydratase beta subunit, N-terminal / Nitrile hydratase alpha subunit /Thiocyanate hydrolase gamma subunit / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase, alpha chain / Nitrile hydratase alpha /Thiocyanate hydrolase gamma superfamily / SH3 type barrels. - #50 / Electron transport accessory-like domain superfamily / Cyclin A; domain 1 / SH3 type barrels. / Roll / Alpha-Beta Complex / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
beta-D-fructofuranose / L(+)-TARTARIC ACID / Thiocyanate hydrolase subunit beta / Thiocyanate hydrolase subunit alpha / Thiocyanate hydrolase subunit gamma
Similarity search - Component
Biological speciesThiobacillus thioparus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.06 Å
AuthorsArakawa, T. / Kawano, Y. / Kataoka, S. / Katayama, Y. / Kamiya, N. / Yohda, M. / Odaka, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure of thiocyanate hydrolase: a new nitrile hydratase family protein with a novel five-coordinate cobalt(III) center.
Authors: Arakawa, T. / Kawano, Y. / Kataoka, S. / Katayama, Y. / Kamiya, N. / Yohda, M. / Odaka, M.
History
DepositionJan 19, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 10, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id
Revision 2.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiocyanate hydrolase alpha subunit
B: Thiocyanate hydrolase beta subunit
C: Thiocyanate hydrolase gamma subunit
D: Thiocyanate hydrolase alpha subunit
E: Thiocyanate hydrolase beta subunit
F: Thiocyanate hydrolase gamma subunit
G: Thiocyanate hydrolase alpha subunit
H: Thiocyanate hydrolase beta subunit
I: Thiocyanate hydrolase gamma subunit
J: Thiocyanate hydrolase alpha subunit
K: Thiocyanate hydrolase beta subunit
L: Thiocyanate hydrolase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,21828
Polymers240,57712
Non-polymers2,64216
Water39,8492212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area78040 Å2
ΔGint-334 kcal/mol
Surface area61220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.307, 175.602, 114.791
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dodecamer as in this record and four equivalent catalytic centers are contained in a molecule.

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Components

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Thiocyanate hydrolase ... , 3 types, 12 molecules ADGJBEHKCFIL

#1: Protein
Thiocyanate hydrolase alpha subunit / SCNase alpha subunit


Mass: 14507.152 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiobacillus thioparus (bacteria) / Strain: THI115 / Plasmid: pET30A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O66187, thiocyanate hydrolase
#2: Protein
Thiocyanate hydrolase beta subunit / SCNase beta subunit


Mass: 18065.549 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiobacillus thioparus (bacteria) / Strain: THI115 / Plasmid: pET30A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O66186, thiocyanate hydrolase
#3: Protein
Thiocyanate hydrolase gamma subunit / SCNase gamma subunit


Mass: 27571.432 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiobacillus thioparus (bacteria) / Strain: THI115 / Plasmid: pET30A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O66188, thiocyanate hydrolase

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Sugars , 1 types, 8 molecules

#4: Sugar
ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose / Fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 2220 molecules

#5: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2212 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5M Na/K Tartrate, 0.1M Potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
2951
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-18B11
SYNCHROTRONSPring-8 BL44B221.2145, 1.2150, 1.2227
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDNov 10, 2004
ADSC QUANTUM 2102CCDNov 25, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
21-m-long platinum-coated bent-cylinder mirror with a fix-exit double crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.21451
31.2151
41.22271
ReflectionResolution: 2→50 Å / Num. all: 222000 / Num. obs: 213749 / % possible obs: 96.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 9.2 Å2
Reflection shellResolution: 2→2.1 Å / % possible all: 91

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.06→32.95 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 217043.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.193 20227 9.9 %RANDOM
Rwork0.165 ---
obs0.165 203583 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.5341 Å2 / ksol: 0.396558 e/Å3
Displacement parametersBiso mean: 15.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.26 Å20 Å20 Å2
2--4.67 Å20 Å2
3----0.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.06→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15689 0 176 2212 18077
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
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
LS refinement shellResolution: 2.06→2.13 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.23 1486 9.5 %
Rwork0.185 14201 -
obs--41 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2fructose.paramfructose.top
X-RAY DIFFRACTION3tartric_acid.paramtartric_acid.top
X-RAY DIFFRACTION4water_rep.paramwater.top

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