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- PDB-7q6a: Crystal structure of Chaetomium thermophilum C30S Ahp1 in post-re... -

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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 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 (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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Sulfate


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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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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

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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

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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

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