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- PDB-2zzd: Recombinant thiocyanate hydrolase, air-oxidized form of holo-enzyme -

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Basic information

Entry
Database: PDB / ID: 2zzd
TitleRecombinant thiocyanate hydrolase, air-oxidized form of holo-enzyme
Components(Thiocyanate hydrolase subunit ...) x 3
KeywordsHYDROLASE / SCNASE / COBALT / METALLOPROTEIN / SULFENIC ACID / SULFINIC ACID / NITRILE HYDRATASE / THIOCYANATE / CARBONYL SULFIDE / CLAW SETTING / PROTEIN / ENZYME / COMPLEX / MODEL COMPLEX / NON-CORRIN / POST-TRANSLATIONAL MODIFICATION / SULFENATE / SULFINATE / CYSTEINE / OXIDATION / AUTOCATALYTIC ACTIVATION / AIR INACTIVATION / Metal-binding
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 / beta-D-glucopyranose / 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 / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsArakawa, T. / Kawano, Y. / Katayama, Y. / Yohda, M. / Odaka, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Structural Basis for Catalytic Activation of Thiocyanate Hydrolase Involving Metal-Ligated Cysteine Modification
Authors: Arakawa, T. / Kawano, Y. / Katayama, Y. / Nakayama, H. / Dohmae, N. / Yohda, M. / Odaka, M.
History
DepositionFeb 9, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)242,38924
Polymers240,83312
Non-polymers1,55712
Water61,2873402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area75430 Å2
ΔGint-394 kcal/mol
Surface area63620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.012, 170.756, 175.176
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE BIOLOGICAL ASSEMBLY IS A SCNASE DODECAMERIC COMPLEX AND FOUR EQUIVALENT CATALYTIC CENTERS ARE CONTAINED IN A MOLECULE.

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Components

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

#1: Protein
Thiocyanate hydrolase subunit alpha


Mass: 14507.152 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiobacillus thioparus (bacteria) / Strain: THI115 / Gene: scnA / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21AI / References: UniProt: O66187, thiocyanate hydrolase
#2: Protein
Thiocyanate hydrolase subunit beta


Mass: 18065.549 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiobacillus thioparus (bacteria) / Strain: THI115 / Gene: scnB / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21AI / References: UniProt: O66186, thiocyanate hydrolase
#3: Protein
Thiocyanate hydrolase subunit gamma


Mass: 27635.428 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiobacillus thioparus (bacteria) / Strain: THI115 / Gene: scnC / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21AI / References: UniProt: O66188, thiocyanate hydrolase

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Sugars , 2 types, 4 molecules

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


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3
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
#7: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 3410 molecules

#5: Chemical
ChemComp-3CO / COBALT (III) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#6: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3402 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHIS PROTEIN CATALYZES THE PRODUCTION OF CARBONYL SULFIDE AND AMMONIA FROM THIOCYANATE.

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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: 3.57 Å3/Da / Density % sol: 65.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 1.5M Na/K Tartrate, 0.1M Potassium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 10, 2006 / Details: Mirror: 11.8m x 1.1m long bent plane mirror of ULE
RadiationMonochromator: 14.5m Triangular Si(111) with an asymmetric angle of 7.8 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 327300 / Num. obs: 319150 / % possible obs: 97.3 % / Observed criterion σ(I): 1.5 / Redundancy: 5.3 % / Biso Wilson estimate: 15.8 Å2 / Rsym value: 0.051 / Net I/σ(I): 13.9 / Num. measured all: 1677550
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 5.1 % / Num. unique all: 30773 / Rsym value: 0.29 / % possible all: 94.6

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DD5

2dd5


Resolution: 1.78→40.76 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 54162.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.159 31002 10 %RANDOM
Rwork0.15 ---
obs0.15 309775 94.3 %-
all-327987 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.5298 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 19.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.62 Å20 Å20 Å2
2---0.28 Å20 Å2
3---2.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.78→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15749 0 92 3402 19243
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.32
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: 1.78→1.89 Å / Rfactor Rfree error: 0.003 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.196 4864 10.1 %
Rwork0.187 43087 -
obs--88.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4fructose.paramfructose.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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