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- PDB-2dd5: Thiocyanate hydrolase (SCNase) from Thiobacillus thioparus native... -

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Basic information

Entry
Database: PDB / ID: 2dd5
TitleThiocyanate hydrolase (SCNase) from Thiobacillus thioparus native holo-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; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase, beta subunit / 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; Chain A / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase, beta subunit / 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
COBALT (III) ION / Thiocyanate hydrolase subunit beta / Thiocyanate hydrolase subunit alpha / Thiocyanate hydrolase subunit gamma
Similarity search - Component
Biological speciesThiobacillus thioparus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.3Oct 25, 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)242,15728
Polymers240,76912
Non-polymers1,38816
Water39,4532190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area75870 Å2
ΔGint-640 kcal/mol
Surface area61890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.187, 170.187, 282.469
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
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 natural source / Source: (natural) Thiobacillus thioparus (bacteria) / Strain: THI 115 / 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 natural source / Source: (natural) Thiobacillus thioparus (bacteria) / Strain: THI 115 / References: UniProt: O66186, thiocyanate hydrolase
#3: Protein
Thiocyanate hydrolase gamma subunit / SCNase gamma subunit containing cobalt centers


Mass: 27619.430 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thiobacillus thioparus (bacteria) / Strain: THI 115 / References: UniProt: O66188, thiocyanate hydrolase

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Non-polymers , 3 types, 2206 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-3CO / COBALT (III) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2190 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 4.24 Å3/Da / Density % sol: 71.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 2.0M ammonium sulfate, 0.1M potassium phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2005
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, direct water cooling using micro-channel (1st crystal), indirect water cooling (2nd crystal)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 278076 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 15.2 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DD4

2dd4


Resolution: 2→37.8 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 1020293.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.205 27732 10.1 %RANDOM
Rwork0.185 ---
obs0.185 275249 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.5731 Å2 / ksol: 0.400868 e/Å3
Displacement parametersBiso mean: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15708 0 64 2190 17962
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.19
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→2.13 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.241 4598 10.2 %
Rwork0.215 40497 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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