[English] 日本語
Yorodumi
- PDB-5oex: Complex with iodine ion for thiocyanate dehydrogenase from Thioal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oex
TitleComplex with iodine ion for thiocyanate dehydrogenase from Thioalkalivibrio paradoxus
ComponentsTHIOCYANATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / THIOCYANATE DEHYDROGENASE / COPPER CENTERS
Function / homologyCytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / WD40/YVTN repeat-like-containing domain superfamily / COPPER (II) ION / IODIDE ION / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Twin-arginine translocation signal domain-containing protein
Function and homology information
Biological speciesThioalkalivibrio paradoxus ARh 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPolyakov, K.M. / Tsallagov, S.I. / Tikhonova, T.V. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Fondation15-14-00063 Russian Federation
CitationJournal: To Be Published
Title: Discovery and characterization of a novel copper containing enzyme - THIOCYANATE DEHYDROGENASE.
Authors: Tikhonova, T.V. / Sorokin, D.I. / Tsallagov, S.I. / Polyakov, K.M. / Trofimov, A.A. / Shabalin, I.G. / Khrenova, M.G. / Muyser, G. / Rakitina, T.V. / Popov, V.O.
History
DepositionJul 10, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionAug 1, 2018ID: 5F30
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.2Jan 17, 2024Group: 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THIOCYANATE DEHYDROGENASE
B: THIOCYANATE DEHYDROGENASE
C: THIOCYANATE DEHYDROGENASE
D: THIOCYANATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,25832
Polymers206,8494
Non-polymers2,40928
Water16,556919
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16850 Å2
ΔGint-253 kcal/mol
Surface area54790 Å2
2
A: THIOCYANATE DEHYDROGENASE
B: THIOCYANATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,69017
Polymers103,4242
Non-polymers1,26615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-119 kcal/mol
Surface area28440 Å2
MethodPISA
3
C: THIOCYANATE DEHYDROGENASE
D: THIOCYANATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,56715
Polymers103,4242
Non-polymers1,14313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-133 kcal/mol
Surface area28450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.820, 159.450, 91.000
Angle α, β, γ (deg.)90.00, 97.77, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
THIOCYANATE DEHYDROGENASE


Mass: 51712.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thioalkalivibrio paradoxus ARh 1 (bacteria)
Gene: THITH_13335 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: W0DP94

-
Non-polymers , 6 types, 947 molecules

#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 919 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: PROTEIN SOLUTION: 10 MG/ML PROTEIN, 25 MM BORATE BUFFER (PH 9.5). PRECIPITANT SOLUTION: 0.025 M AMMONIUM IODIDE, 20.0 % W/V PEG 3350. VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 124180 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / CC1/2: 0.996 / Rpim(I) all: 0.155 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.35 / Num. unique obs: 9243 / CC1/2: 0.764 / Rpim(I) all: 0.861 / % possible all: 94.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F30

5f30
PDB Unreleased entry


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.97 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.19841 6102 4.9 %RANDOM
Rwork0.15573 ---
obs0.15784 118078 93.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.175 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å2-0.47 Å2
2---1.02 Å2-0 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14572 0 52 919 15543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01915082
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0181.94220529
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.32251869
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27524.456671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.593152358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7461570
X-RAY DIFFRACTIONr_chiral_restr0.1430.22225
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02111598
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6521.9377474
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3442.8959337
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9082.1717608
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.3679.20624141
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 403 -
Rwork0.261 8827 -
obs--94.39 %

+
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