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- PDB-2dxb: Recombinant thiocyanate hydrolase comprising partially-modified c... -

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Basic information

Entry
Database: PDB / ID: 2dxb
TitleRecombinant thiocyanate hydrolase comprising partially-modified cobalt centers
Components(Thiocyanate hydrolase subunit ...) x 3
KeywordsHYDROLASE / 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
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 / PHOSPHATE 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: 2.25 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
DepositionAug 25, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details

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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
M: Thiocyanate hydrolase subunit alpha
N: Thiocyanate hydrolase subunit beta
O: Thiocyanate hydrolase subunit gamma
P: Thiocyanate hydrolase subunit alpha
Q: Thiocyanate hydrolase subunit beta
R: Thiocyanate hydrolase subunit gamma
S: Thiocyanate hydrolase subunit alpha
T: Thiocyanate hydrolase subunit beta
U: Thiocyanate hydrolase subunit gamma
V: Thiocyanate hydrolase subunit alpha
W: Thiocyanate hydrolase subunit beta
X: Thiocyanate hydrolase subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)482,76840
Polymers481,53724
Non-polymers1,23116
Water52,9822941
1
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)241,38420
Polymers240,76912
Non-polymers6168
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area74060 Å2
ΔGint-434 kcal/mol
Surface area62190 Å2
MethodPISA, PQS
2
M: Thiocyanate hydrolase subunit alpha
N: Thiocyanate hydrolase subunit beta
O: Thiocyanate hydrolase subunit gamma
P: Thiocyanate hydrolase subunit alpha
Q: Thiocyanate hydrolase subunit beta
R: Thiocyanate hydrolase subunit gamma
S: Thiocyanate hydrolase subunit alpha
T: Thiocyanate hydrolase subunit beta
U: Thiocyanate hydrolase subunit gamma
V: Thiocyanate hydrolase subunit alpha
W: Thiocyanate hydrolase subunit beta
X: Thiocyanate hydrolase subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,38420
Polymers240,76912
Non-polymers6168
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area73910 Å2
ΔGint-433 kcal/mol
Surface area62340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)114.874, 245.141, 244.653
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 (CHAIN A-L AND M-X OF THIS RECORD) AND FOUR EQUIVALENT CATALYTIC CENTERS ARE CONTAINED IN A MOLECULE

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Components

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Thiocyanate hydrolase subunit ... , 3 types, 24 molecules ADGJMPSVBEHKNQTWCFILORUX

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


Mass: 14507.152 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiobacillus thioparus (bacteria) / Strain: THI115 / Plasmid: pET32a / 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 subunit beta / SCNase beta subunit


Mass: 18065.549 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiobacillus thioparus (bacteria) / Strain: THI115 / Plasmid: pET32a / 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 subunit gamma / SCNase gamma subunit containing cobalt centers


Mass: 27619.430 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiobacillus thioparus (bacteria) / Strain: THI115 / Plasmid: pET32a / 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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Non-polymers , 3 types, 2957 molecules

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


Mass: 58.933 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Co
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2941 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 3.85 Å3/Da / Density % sol: 68.09 %
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: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 10, 2004
RadiationMonochromator: Diamond crystals; First crystal is in Laue setting, and second one is in Bragg setting
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 324000 / Num. obs: 322968 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 11.3 Å2 / Rsym value: 0.099 / Net I/σ(I): 0.085
Reflection shellResolution: 2.25→2.33 Å / Rsym value: 0.208 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DD5

2dd5


Resolution: 2.25→49.41 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 327805.92 / 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
Rfree0.198 31794 10 %RANDOM
Rwork0.171 ---
obs0.171 316929 97.6 %-
all-324000 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.419 Å2 / ksol: 0.393681 e/Å3
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1--6.22 Å20 Å20 Å2
2--4.39 Å20 Å2
3---1.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.25→49.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31402 0 48 2941 34391
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.682
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.003 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.219 5076 10.2 %
Rwork0.181 44591 -
obs--92.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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