[English] 日本語
Yorodumi
- PDB-8p3l: The structure of thiocyanate dehydrogenase mutant form with Thr 1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8p3l
TitleThe structure of thiocyanate dehydrogenase mutant form with Thr 169 replaced by Ala from Thioalkalivibrio paradoxus
ComponentsTwin-arginine translocation signal domain-containing protein
KeywordsOXIDOREDUCTASE / Thiocyanate dehydrogenase / Thioalkalivibrio paradoxus / Recombinant protein / Surface amino acid residue mutation
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 / metal ion binding / COPPER (II) ION / Twin-arginine translocation signal domain-containing protein
Function and homology information
Biological speciesThioalkalivibrio paradoxus ARh 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVarfolomeeva, L.A. / Polyakov, K.M. / Komolov, A.S. / Rakitina, T.V. / Dergousova, N.I. / Dorovatovskii, P.V. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation23-74-30004 Russian Federation
CitationJournal: Crystallography Reports / Year: 2023
Title: Improvement of the Diffraction Properties of Thiocyanate Dehydrogenase Crystals
Authors: Varfolomeeva, L.A. / Polyakov, K.M. / Komolov, A.S. / Rakitina, T.V. / Dergousova, N.I. / Dorovatovskii, P.V. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O.
History
DepositionMay 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Twin-arginine translocation signal domain-containing protein
D: Twin-arginine translocation signal domain-containing protein
G: Twin-arginine translocation signal domain-containing protein
J: Twin-arginine translocation signal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,16820
Polymers219,8914
Non-polymers1,27716
Water13,385743
1
A: Twin-arginine translocation signal domain-containing protein
D: Twin-arginine translocation signal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4889
Polymers109,9452
Non-polymers5427
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-161 kcal/mol
Surface area28570 Å2
MethodPISA
2
G: Twin-arginine translocation signal domain-containing protein
J: Twin-arginine translocation signal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,68011
Polymers109,9452
Non-polymers7349
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-148 kcal/mol
Surface area28390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.810, 162.240, 90.760
Angle α, β, γ (deg.)90.00, 119.74, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Twin-arginine translocation signal domain-containing protein / Thiocyanate dehydrogenase


Mass: 54972.668 Da / Num. of mol.: 4 / Mutation: T169A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thioalkalivibrio paradoxus ARh 1 (bacteria)
Gene: THITH_13335 / Production host: Escherichia coli (E. coli) / References: UniProt: W0DP94
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.2 M (NH4)2SO4, 0.1 M Bis-Tris, pH5.5, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.79312 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.79312 Å / Relative weight: 1
ReflectionResolution: 1.8→81.12 Å / Num. obs: 208077 / % possible obs: 98.8 % / Redundancy: 6.7 % / CC1/2: 0.987 / Rmerge(I) obs: 0.252 / Rrim(I) all: 0.273 / Net I/σ(I): 6.57
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.8-1.851.187147190.721.291
1.85-1.90.961149950.8031.0411
1.9-1.950.81144180.8230.8781
1.95-2.010.61141230.8990.6591
2.01-2.080.544137190.9050.5891
2.08-2.150.474132620.9230.5121
2.15-2.230.436128640.9340.4721
2.23-2.320.402123870.9390.4351
2.32-2.430.365117960.9520.3951
2.43-2.550.322113880.9580.3491
2.55-2.680.301108170.960.3261
2.68-2.850.253102450.9720.2741
2.85-3.040.2196390.980.2271
3.04-3.290.17189600.9830.1851
3.29-3.60.13782810.9870.1491
3.6-4.030.12274950.9880.1321
4.03-4.650.166090.9920.1091
4.65-5.690.09756260.9920.1051
5.69-8.050.11143300.9920.121
8.05-81.120.07324040.9970.0791

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→81.12 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.887 / SU B: 2.38 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25409 10643 5.1 %RANDOM
Rwork0.18641 ---
obs0.18986 197378 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.867 Å2
Baniso -1Baniso -2Baniso -3
1--6.24 Å2-0 Å2-2.52 Å2
2--29.47 Å20 Å2
3----23.22 Å2
Refinement stepCycle: 1 / Resolution: 1.8→81.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14527 0 48 743 15318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01215010
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.0011.63520451
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.30151864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22223.352722
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.006152300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3721562
X-RAY DIFFRACTIONr_chiral_restr0.2190.21909
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.0211646
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_it3.0241.8317468
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.8822.7519328
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2337542
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.39525.57624252
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: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 794 -
Rwork0.243 13667 -
obs--92.95 %

+
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