[English] 日本語
Yorodumi
- PDB-7q6a: Crystal structure of Chaetomium thermophilum C30S Ahp1 in post-re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q6a
TitleCrystal structure of Chaetomium thermophilum C30S Ahp1 in post-reaction state
ComponentsThioredoxin domain-containing protein
KeywordsOXIDOREDUCTASE / urmylation / Urm1 / ubiquitin-like
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 24, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: 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.year
Revision 1.2Sep 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 1.3Oct 26, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Jan 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
B: Thioredoxin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,94512
Polymers36,0012
Non-polymers94510
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-81 kcal/mol
Surface area14530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.842, 41.101, 60.820
Angle α, β, γ (deg.)77.090, 75.120, 67.270
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Thioredoxin domain-containing protein


Mass: 18000.326 Da / Num. of mol.: 2 / Mutation: C30S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0014370 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S1P8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.01 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6
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: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.1→32.46 Å / Num. obs: 112459 / % possible obs: 89.3 % / Redundancy: 3.702 % / Biso Wilson estimate: 15.437 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.068 / Χ2: 0.841 / Net I/σ(I): 10.94 / Num. measured all: 416316 / Scaling rejects: 46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.123.6411.3820.9727082934374380.4641.60879.6
1.12-1.163.711.0821.3229526909179590.5591.25887.5
1.16-1.193.6730.8821.628359885677210.6311.02887.2
1.19-1.233.5780.7491.8425728856771900.6990.87783.9
1.23-1.273.7710.6212.328294829775040.7760.72190.4
1.27-1.313.7590.4842.8827058801371990.850.56289.8
1.31-1.363.7490.4013.3926403777270430.8870.46690.6
1.36-1.413.740.3194.225042747566960.920.37289.6
1.41-1.483.5680.245.3621771715261010.9450.28185.3
1.48-1.553.7710.1667.7824009686163670.9740.19492.8
1.55-1.633.790.12310.1723050652760820.9860.14393.2
1.63-1.733.7610.09512.9821522614657220.9910.1193.1
1.73-1.853.7280.07216.6319851575853250.9940.08492.5
1.85-23.5210.05221.2316850538747860.9970.06188.8
2-2.193.6380.03827.9416324496944870.9980.04590.3
2.19-2.453.7640.03432.6215942445642350.9980.03995
2.45-2.833.7670.0336.0114125395937500.9980.03594.7
2.83-3.473.6560.02939.9511303333330920.9980.03492.8
3.47-4.93.6430.02743.488611257623640.9980.03291.8
4.9-32.463.910.02545.785466142113980.9990.02998.4

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DSR

4dsr


Resolution: 1.1→32.46 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 19.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1739 5612 4.99 %
Rwork0.1614 106838 -
obs0.162 112450 89.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.41 Å2 / Biso mean: 19.7503 Å2 / Biso min: 6.64 Å2
Refinement stepCycle: final / Resolution: 1.1→32.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2466 0 79 449 2994
Biso mean--48.89 30.66 -
Num. residues----335
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.110.34391320.35742826295870
1.11-1.120.30591800.29843476365688
1.12-1.140.29812030.29413452365588
1.14-1.150.3032010.29533550375188
1.15-1.160.30391660.27053489365587
1.16-1.180.26851860.26993432361887
1.18-1.20.25211740.25523493366786
1.2-1.220.26971710.2543184335581
1.22-1.230.24132080.24253550375889
1.23-1.250.2481790.23373593377290
1.25-1.280.22551990.21973581378090
1.28-1.30.23661630.21233607377090
1.3-1.320.21871940.20793643383790
1.32-1.350.20272040.20463578378291
1.35-1.380.2381840.19353656384090
1.38-1.410.18191890.1863487367689
1.41-1.450.18921950.18543501369688
1.45-1.490.18081730.17693393356684
1.49-1.530.16742000.15263666386693
1.53-1.580.1691850.15273726391193
1.58-1.640.15411960.14253755395194
1.64-1.70.15751830.14773712389593
1.7-1.780.16351880.1493738392693
1.78-1.870.17352040.1433643384792
1.87-1.990.15591820.13973515369789
1.99-2.140.14531820.13633541372388
2.15-2.360.14452000.13093776397695
2.36-2.70.15122000.13493805400595
2.7-3.40.1691880.1423721390993
3.4-32.460.14362030.14023749395294
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)
11.08460.3867-0.10132.89810.90641.0613-0.01430.0424-0.0216-0.015-0.01720.1310.0306-0.05220.04540.06220.0066-0.02340.07260.00720.0686-29.6713-2.6046-22.4139
23.3039-0.1812-0.15615.1646-0.28883.96650.0138-0.02330.079-0.06150.0321-0.261-0.0570.2807-0.04320.0766-0.0029-0.00730.0836-0.00950.1043-13.82695.8309-17.9982
32.41590.66261.31413.01511.31593.9195-0.08280.44980.1761-0.44820.07480.0407-0.3217-0.16660.01070.15260.00020.0170.17170.02850.0825-18.56734.7335-33.641
41.07240.2805-0.07921.66150.60711.19820.00610.11830.073-0.1634-0.01280.0641-0.0771-0.04270.00370.0750.0087-0.01080.06760.00720.0798-25.74934.8456-22.8643
52.24580.7754-0.23133.55210.36541.464-0.0271-0.0947-0.17650.29760.0333-0.07720.11150.0594-0.01150.09870.0125-0.01970.07120.01050.0957-19.92-7.744-14.0009
66.91511.10494.29623.82742.07656.62720.03860.3897-0.2754-0.18530.0456-0.08780.08790.0885-0.09520.08750.00070.01450.0646-0.02520.0851-20.9675-10.83-29.4147
76.9393-1.71586.2747.7312-3.8656.92240.11330.0251-0.2097-0.023-0.0147-0.32110.16070.0899-0.11320.06790.00610.01740.1244-0.03090.1327-7.9027-4.059-22.1178
82.84730.81152.78768.25753.75053.85150.05430.5963-0.434-0.59470.1999-0.33240.4218-0.1282-0.24090.2141-0.02990.03910.2105-0.04390.1308-13.952-4.8615-35.7198
91.32380.1294-0.36930.9593-0.00132.61550.1038-0.42380.07560.1852-0.0858-0.00710.00260.2658-0.03450.1149-0.0502-0.00230.1915-0.03080.0987-14.260915.40693.0465
101.11770.12420.63854.92472.63363.81450.08-0.15930.3706-0.02-0.0770.193-0.3933-0.18380.0520.12940.00110.05150.1139-0.03710.183-28.258121.7748-2.5096
111.55620.0908-0.45220.54230.15562.22470.0971-0.26960.08730.1482-0.07210.0403-0.02640.0775-0.01960.0861-0.03170.00950.0989-0.01590.0708-20.478713.5622-0.4964
122.37081.73672.61962.91652.48883.29180.0952-0.57340.16860.2478-0.1120.2256-0.17280.15280.08940.1813-0.09720.04440.3359-0.07280.0728-24.728917.633712.1085
136.51183.05891.545.1512-3.1658.47270.3416-0.40650.16340.041-0.05320.33010.1059-0.3614-0.18970.0928-0.00380.02920.1878-0.0410.1638-36.653614.66794.2938
144.4916-3.39480.02487.91752.84978.6269-0.1388-0.78070.36830.71930.0690.363-0.4891-0.23120.17160.2858-0.04460.13140.2791-0.17140.2736-30.334526.808610.1677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 51 )A1 - 51
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 63 )A52 - 63
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 77 )A64 - 77
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 113 )A78 - 113
5X-RAY DIFFRACTION5chain 'A' and (resid 114 through 132 )A114 - 132
6X-RAY DIFFRACTION6chain 'A' and (resid 133 through 147 )A133 - 147
7X-RAY DIFFRACTION7chain 'A' and (resid 148 through 158 )A148 - 158
8X-RAY DIFFRACTION8chain 'A' and (resid 159 through 168 )A159 - 168
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 51 )B2 - 51
10X-RAY DIFFRACTION10chain 'B' and (resid 52 through 77 )B52 - 77
11X-RAY DIFFRACTION11chain 'B' and (resid 78 through 131 )B78 - 131
12X-RAY DIFFRACTION12chain 'B' and (resid 132 through 148 )B132 - 148
13X-RAY DIFFRACTION13chain 'B' and (resid 149 through 158 )B149 - 158
14X-RAY DIFFRACTION14chain 'B' and (resid 159 through 168 )B159 - 168

+
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