[English] 日本語
Yorodumi
- PDB-2dxc: Recombinant thiocyanate hydrolase, fully-matured form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2dxc
TitleRecombinant thiocyanate hydrolase, fully-matured form
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 / 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: 1.9 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 30, 2024Group: Structure summary / Category: pdbx_entry_details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)241,60520
Polymers240,76912
Non-polymers8368
Water45,5962531
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area74570 Å2
ΔGint-405 kcal/mol
Surface area62280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)114.874, 170.531, 175.152
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 AND FOUR EQUIVALENT CATALYTIC CENTERS ARE CONTAINED IN A MOLECULE

-
Components

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

#1: Protein
Thiocyanate hydrolase subunit alpha / 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: 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.: 4
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.: 4
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

-
Non-polymers , 3 types, 2539 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.: 2531 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.46 %
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

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 6, 2005
Details: Rhodium coated silicon single crystal (Flat shaped, 1000mm(L) x 100mm(W) x 70mm(T)) with 3.5mrad glancing angle
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 269900 / Num. obs: 263483 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Biso Wilson estimate: 10.8 Å2 / Rsym value: 0.044
Reflection shellResolution: 1.9→1.97 Å / Rsym value: 0.158 / % possible all: 93.1

-
Processing

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

2dd5


Resolution: 1.9→41.85 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 242999.73 / 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 26126 10 %RANDOM
Rwork0.171 ---
obs0.171 260988 96.8 %-
all-269600 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.8588 Å2 / ksol: 0.380175 e/Å3
Displacement parametersBiso mean: 16.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.39 Å20 Å20 Å2
2---0.8 Å20 Å2
3---4.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.9→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15708 0 44 2531 18283
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_d22.3
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_it0.991.5
X-RAY DIFFRACTIONc_mcangle_it1.452
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.692.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.003 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.207 4149 10.2 %
Rwork0.19 36549 -
obs--91.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2tartric_acid.paramtartric_acid.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more