[English] 日本語
Yorodumi
- PDB-7q68: Crystal structure of Chaetomium thermophilum wild-type Ahp1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q68
TitleCrystal structure of Chaetomium thermophilum wild-type Ahp1
ComponentsThioredoxin domain-containing protein
KeywordsOXIDOREDUCTASE / urmylation / Urm1 / ubiquitin-like
Function / homology
Function and homology information


thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / peroxisome / cellular response to oxidative stress / mitochondrion / metal ion binding
Similarity search - Function
Peroxiredoxin-5-like / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Thioredoxin domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRavichandran, K.E. / Wilk, P. / Grudnik, P. / Glatt, S.
Funding support Poland, 4items
OrganizationGrant numberCountry
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6 Poland
European Research Council (ERC)101001394 Poland
Polish National Science Centre2018/31/B/NZ1/03559 Poland
Foundation for Polish ScienceFirstTEAM/2016-1/2 Poland
CitationJournal: Embo J. / Year: 2022
Title: E2/E3-independent ubiquitin-like protein conjugation by Urm1 is directly coupled to cysteine persulfidation.
Authors: Ravichandran, K.E. / Kaduhr, L. / Skupien-Rabian, B. / Shvetsova, E. / Sokolowski, M. / Krutyholowa, R.C. / Kwasna, D. / Brachmann, C. / Lin, S. / Guzman Perez, S. / Wilk, P. / Kosters, M. / ...Authors: Ravichandran, K.E. / Kaduhr, L. / Skupien-Rabian, B. / Shvetsova, E. / Sokolowski, M. / Krutyholowa, R.C. / Kwasna, D. / Brachmann, C. / Lin, S. / Guzman Perez, S. / Wilk, P. / Kosters, M. / Grudnik, P. / Jankowska, U. / Leidel, S.A. / Schaffrath, R. / Glatt, S.
History
DepositionNov 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 26, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5857
Polymers18,0161
Non-polymers5686
Water1,820101
1
A: Thioredoxin domain-containing protein
hetero molecules

A: Thioredoxin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,17014
Polymers36,0332
Non-polymers1,13712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+3/41
Buried area3890 Å2
ΔGint-113 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.249, 75.249, 110.241
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Components on special symmetry positions
IDModelComponents
11A-471-

HOH

21A-493-

HOH

31A-500-

HOH

-
Components

#1: Protein Thioredoxin domain-containing protein


Mass: 18016.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0014370 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S1P8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2 M Ammonium Sulfate and 0.1 M Sodium cacodylate -pH 6.5.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.75→47.92 Å / Num. obs: 32659 / % possible obs: 99.8 % / Redundancy: 9.329 % / Biso Wilson estimate: 39.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.071 / Net I/σ(I): 14.81
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 9.456 % / Rmerge(I) obs: 1.883 / Mean I/σ(I) obs: 0.84 / Num. unique obs: 5130 / CC1/2: 0.719 / Rrim(I) all: 1.991 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DSR

4dsr


Resolution: 1.75→47.92 Å / SU ML: 0.2505 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4544
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2019 1629 5 %
Rwork0.1878 30961 -
obs0.1885 32590 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.59 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1246 0 32 101 1379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00491305
X-RAY DIFFRACTIONf_angle_d0.58361777
X-RAY DIFFRACTIONf_chiral_restr0.0481204
X-RAY DIFFRACTIONf_plane_restr0.0044227
X-RAY DIFFRACTIONf_dihedral_angle_d19.6166453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80.39671290.37312477X-RAY DIFFRACTION98.27
1.8-1.860.38571320.3372534X-RAY DIFFRACTION99.66
1.86-1.920.34311340.30082541X-RAY DIFFRACTION99.66
1.92-20.26341330.2422514X-RAY DIFFRACTION99.36
2-2.090.2241360.21272560X-RAY DIFFRACTION99.59
2.09-2.20.23621340.19052557X-RAY DIFFRACTION99.89
2.2-2.340.24341340.18152555X-RAY DIFFRACTION99.67
2.34-2.520.19131360.19372578X-RAY DIFFRACTION99.85
2.52-2.780.21141360.20322586X-RAY DIFFRACTION100
2.78-3.180.22681380.20062609X-RAY DIFFRACTION99.93
3.18-40.18321390.17432646X-RAY DIFFRACTION99.79
4-47.920.16991480.16422804X-RAY DIFFRACTION99.76
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.571676767051.644037793485.042440773321.958219251852.09529656773.977009526770.06560510087490.482623725013-0.1612215352540.280172605820.113213936949-0.3973854382020.04809533073510.884140819898-0.3194336673840.35663273864-0.0273129456543-0.02414777076880.5720095720730.06292938717320.3608275276834.970288661870.196429243341.5230573713
24.5211496913-4.71439510923-3.553201172545.019548058544.484952153967.580897161860.02166415355460.288437956039-0.251997423241-0.0533298318755-0.23659791450.4122097414390.559055395726-0.8951199790540.2336085628820.347218512191-0.03091056965330.004356905113610.5000558198050.01518030583970.44665662060110.292447413773.097113227831.4232917196
38.505537498674.67194925491.603480342658.379565304650.2292307200251.41423297828-0.3770546059340.408941841830.248459237312-0.3044571107650.108130477705-0.408114541369-1.08627772091.051789653590.2552777232810.323761326696-0.0805058954111-0.05173384160870.4607732209190.1173773177780.32985223722129.592924301476.357557931837.0919595436
43.917961227442.471053299590.2736783589188.781068344154.623839220832.996477278060.0491491581568-2.125691591580.5463247256482.33228549569-0.6053389280591.1587535380.227517912624-0.6789691856260.570882758260.767706237407-0.01054505505250.1615362315740.828823439421-0.07682193719330.52351959526813.683110605968.31705104952.15625923
54.374808499760.1310223378091.219833142441.99492112813-0.481236524084.35414160458-0.172734659276-0.1701297353090.2251414671940.1547062382780.0023772868676-0.0541296725302-0.3628210366370.1366856189580.1715878004120.3644434837590.00257734504617-0.009337547009740.3746535567830.02905835650640.32259556643921.006871895973.259413108543.6146071547
66.681818586460.5396559712950.3507086619733.8387836814-0.6265782824116.95192302458-0.167899888592-0.06245430654070.5501342522340.37630088328-0.00442308301881-0.311404063402-0.6736532855570.5829315188720.2586940647950.356094739921-0.0834591954243-0.1133261337150.5012139795150.04670811451560.40969648944832.502872605375.643110843448.6196424839
79.142548579220.9168955312290.5571418099512.39464947531-1.298028219869.33364670993-0.426780016024-1.282015511870.3534900673070.174662492433-0.201805132961-0.112209116009-0.8540824865870.06327831408030.6722447947330.5576132960750.0133456929922-0.1076997751120.653591985673-0.06592895010930.43131701915326.764991945377.530631677656.3334544459
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 18 )1 - 181 - 18
22chain 'A' and (resid 19 through 33 )19 - 3319 - 33
33chain 'A' and (resid 34 through 51 )34 - 5134 - 51
44chain 'A' and (resid 52 through 63 )52 - 6352 - 63
55chain 'A' and (resid 64 through 131 )64 - 13164 - 132
66chain 'A' and (resid 132 through 148 )132 - 148133 - 149
77chain 'A' and (resid 149 through 169 )149 - 169150 - 170

+
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