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- PDB-3vyg: Crystal structure of Thiocyanate hydrolase mutant R136W -

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Basic information

Entry
Database: PDB / ID: 3vyg
TitleCrystal structure of Thiocyanate hydrolase mutant R136W
Components(Thiocyanate hydrolase subunit ...) x 3
KeywordsHYDROLASE / Thiocyanate hydrolase / Cysteine-sulfenic acid / Cysteine-sulfic acid / metalloenzyme
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 / 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: 1.72 Å
AuthorsYamanaka, Y. / Sato, M. / Arakawa, T. / Namima, S. / Hori, S. / Ohtaki, A. / Noguchi, K. / Katayama, Y. / Yohda, M. / Odaka, M.
CitationJournal: To be published
Title: Effects of argnine residue around the substrate pocket on the substrate specificity of thiocyanate hydrolase
Authors: Yamanaka, Y. / Sato, M. / Arakawa, T. / Namima, S. / Hori, S. / Ohtaki, A. / Noguchi, K. / Katayama, Y. / Yohda, M. / Odaka, M.
History
DepositionSep 25, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)241,72120
Polymers240,88512
Non-polymers8368
Water27,0231500
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area74050 Å2
ΔGint-364 kcal/mol
Surface area64040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.448, 172.398, 172.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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) / Gene: scnA / Production host: Escherichia coli (E. coli) / 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) / Gene: scnB / Production host: Escherichia coli (E. coli) / References: UniProt: O66186, thiocyanate hydrolase
#3: Protein
Thiocyanate hydrolase subunit gamma


Mass: 27648.445 Da / Num. of mol.: 4 / Mutation: R136W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiobacillus thioparus (bacteria) / Gene: scnC / Production host: Escherichia coli (E. coli) / References: UniProt: O66188, thiocyanate hydrolase

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Non-polymers , 3 types, 1508 molecules

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


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


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


Mass: 18.015 Da / Num. of mol.: 1500 / 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: 3.5 Å3/Da / Density % sol: 64.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1M potassium phosphate pH 6.8, 1.4M potassium phosphate tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 17, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. all: 343322 / Num. obs: 325674 / % possible obs: 96.5 % / Rmerge(I) obs: 0.062
Reflection shellResolution: 1.72→1.78 Å / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 9.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DD5

2dd5


Resolution: 1.72→33.96 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 1.626 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21771 17284 5 %RANDOM
Rwork0.18746 ---
obs0.18899 325672 96.45 %-
all-343322 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.084 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.72→33.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15702 0 44 1500 17246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.02216167
X-RAY DIFFRACTIONr_angle_refined_deg2.3111.95322071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.2465.0411975
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45523.176762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.058152578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.93115140
X-RAY DIFFRACTIONr_chiral_restr0.1870.22423
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02112524
X-RAY DIFFRACTIONr_mcbond_it1.4531.59835
X-RAY DIFFRACTIONr_mcangle_it2.215215994
X-RAY DIFFRACTIONr_scbond_it3.24536332
X-RAY DIFFRACTIONr_scangle_it4.8334.56072
LS refinement shellResolution: 1.721→1.766 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 1227 -
Rwork0.231 24556 -
obs--99.22 %

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