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- PDB-7q69: Crystal structure of Chaetomium thermophilum C30S Ahp1 in the pre... -

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Basic information

Entry
Database: PDB / ID: 7q69
TitleCrystal structure of Chaetomium thermophilum C30S Ahp1 in the pre-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: 1.85 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
C: Thioredoxin domain-containing protein
D: Thioredoxin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,75117
Polymers72,5144
Non-polymers1,23713
Water16,159897
1
A: Thioredoxin domain-containing protein
B: Thioredoxin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9259
Polymers36,2572
Non-polymers6687
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-77 kcal/mol
Surface area15150 Å2
MethodPISA
2
C: Thioredoxin domain-containing protein
D: Thioredoxin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8258
Polymers36,2572
Non-polymers5686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-39 kcal/mol
Surface area14640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.139, 101.727, 69.419
Angle α, β, γ (deg.)90.000, 107.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thioredoxin domain-containing protein


Mass: 18128.457 Da / Num. of mol.: 4 / Mutation: C30S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / 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.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 897 / 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: 2.8 Å3/Da / Density % sol: 56 %
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

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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: Oct 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.85→46.07 Å / Num. obs: 65645 / % possible obs: 96.1 % / Redundancy: 3.339 % / Biso Wilson estimate: 26.797 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.117 / Rrim(I) all: 0.14 / Χ2: 0.877 / Net I/σ(I): 11.24 / Num. measured all: 219199 / Scaling rejects: 258
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
1.85-1.92.6070.7871.8410507503340310.5390.99180.1
1.9-1.952.9280.7512.612778487643640.6310.92189.5
1.95-23.5270.6123.6416749479347490.7910.72299.1
2-2.073.5070.5144.5715954461845490.8040.60898.5
2.07-2.133.4250.4035.4415072449844000.8650.47997.8
2.13-2.213.4290.3266.2314791437643140.9020.38798.6
2.21-2.293.1140.4196.3612140416738980.8530.50993.5
2.29-2.383.5770.2298.1814466407340440.9560.2799.3
2.38-2.493.5440.1839.5813616387138420.9690.21699.3
2.49-2.613.4860.15910.4712792372136700.9740.18898.6
2.61-2.753.2460.13711.7311168354134410.9750.16497.2
2.75-2.923.4910.10814.111446330632790.9870.12799.2
2.92-3.123.530.08317.3310958313231040.9910.09899.1
3.12-3.373.4770.06620.1610115294929090.9950.07898.6
3.37-3.693.1270.05822.178099269525900.9950.0796.1
3.69-4.133.4640.04826.078289243823930.9960.05798.2
4.13-4.773.4050.03829.887255216921310.9970.04598.2
4.77-5.843.2160.03927.235670182517630.9960.04796.6
5.84-8.263.4610.038294842142113990.9970.04498.5
8.26-46.073.2150.02733.5124928087750.9980.03395.9

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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: 1.85→46.07 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1828 3281 5 %
Rwork0.1571 62290 -
obs0.1584 65571 96.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.51 Å2 / Biso mean: 28.1559 Å2 / Biso min: 9.45 Å2
Refinement stepCycle: final / Resolution: 1.85→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4979 0 83 897 5959
Biso mean--49.01 34.45 -
Num. residues----676
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.870.3321130.2952167228076
1.87-1.90.30391250.27712366249187
1.9-1.940.3681320.28282501263387
1.94-1.970.22181420.20252697283998
1.97-20.20611480.17122814296299
2-2.040.18421460.16722778292499
2.04-2.080.2181450.18462696284196
2.08-2.130.2011450.16262764290999
2.13-2.180.20771460.16252782292899
2.18-2.230.21211460.17272746289297
2.23-2.290.18371320.17622556268892
2.29-2.360.20171480.15082811295999
2.36-2.440.16811470.14082798294599
2.44-2.530.18031480.14562793294199
2.53-2.630.18791460.14842785293199
2.63-2.750.18321460.15222762290897
2.75-2.890.18861460.15232769291599
2.89-3.070.18151470.15072804295199
3.07-3.310.14811480.15232808295699
3.31-3.640.1671430.14022731287497
3.64-4.170.13941460.12612756290298
4.17-5.250.1381470.1172787293498
5.25-46.070.18731490.17862819296898
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)
17.61952.00321.08685.17251.39666.58950.0537-0.3235-0.56060.3166-0.0085-0.32450.48780.1682-0.04350.1650.00870.0190.17350.04120.2713-22.02765.9021-8.5423
25.90951.79-3.60451.0673-1.03463.49850.1569-0.33250.2307-0.0088-0.0629-0.0113-0.19810.3629-0.08740.13330.0105-0.00730.16540.01810.1667-5.936422.353-18.4831
34.98890.4174-0.05521.25190.04551.87910.03620.0087-0.339-0.03750.00640.050.04590.0215-0.0380.109-0.01120.00240.08070.03060.0888-9.371312.9023-18.9307
47.7742-1.12185.40152.71130.38768.68650.22610.5344-0.175-0.3553-0.0397-0.11540.20610.1233-0.1740.2122-0.02520.03480.2234-0.04870.1931-10.06838.2726-31.2947
53.4130.4326-0.30521.2049-0.21591.32260.0264-0.02320.0089-0.04620.00960.01360.01170.0617-0.04260.08440.00490.01170.07530.00910.1199-6.446415.4997-19.1127
64.50031.0268-0.48651.54590.04832.01050.1859-0.2503-0.91460.2102-0.0839-0.20810.26720.1357-0.01830.1407-0.0119-0.01260.17150.09160.251-6.96545.3811-9.0537
77.9364-4.4812-2.27847.9130.60512.06860.24010.3087-0.3861-0.2111-0.2920.29590.115-0.08190.01740.0997-0.02660.00150.1127-0.00430.1508-19.85317.1319-18.1623
86.4127-3.8842-0.14682.7697-0.75422.0946-0.0101-0.4479-1.12730.2923-0.0032-0.01980.43560.31250.00310.19190.0114-0.03430.21470.04050.4436-7.3386-2.9299-17.8045
97.92273.7811-0.82173.20182.71728.29430.37290.1744-0.0523-0.3531-0.0128-0.0096-0.0164-0.3104-0.32050.2332-0.0123-0.01160.1582-0.03730.2197-20.01612.4764-28.3741
102.68461.45582.10213.25930.90391.92060.0178-0.41070.01970.3038-0.1098-0.0221-0.0329-0.32180.22840.16460.01430.03320.2006-0.01120.113123.149315.01420.6243
111.876-0.6521.91251.0339-0.972.05670.11960.1449-0.0529-0.11220.01330.2090.08090.0381-0.12270.1790.0230.00390.1931-0.03670.207513.25066.9335-22.9348
122.67540.02210.98991.0878-0.15941.1247-0.0350.00290.08250.0009-0.0277-0.0212-0.0707-0.00610.02690.11590.00770.01260.148-0.01920.11319.29816.6563-10.3551
134.5093-1.11921.46771.7477-0.5471.4082-0.05510.40650.421-0.2657-0.1013-0.3385-0.05670.14580.12640.1687-0.02370.02590.15730.03030.180726.687624.7116-17.6586
142.68320.11980.93891.7446-0.39840.87120.03740.14710.014-0.10140.0005-0.0456-0.01960.04510.00460.1126-0.00260.01510.1388-0.02090.118616.265214.6454-16.0415
151.9553-0.83490.35511.74250.04891.5741-0.0675-0.19380.07810.10410.00020.16210.0084-0.18460.05680.1446-0.00490.01350.1769-0.0360.119616.707618.6488-1.6475
169.0988-4.2803-0.01935.39760.60472.1375-0.1071-0.31240.20830.16870.1028-0.237-0.12480.17460.06280.1254-0.0058-0.0090.163-0.04420.15125.266224.7763-1.3623
177.4237-0.0014-0.49885.33410.24865.3463-0.0777-0.32670.43240.0862-0.0182-0.2097-0.45520.08720.10350.174-0.0402-0.03070.1182-0.02960.148522.940730.9702-7.676
180.1446-0.69080.52523.198-2.66542.3345-0.3265-0.13470.31770.7034-0.1586-0.707-0.51980.11920.41310.24290.0146-0.09320.1592-0.00080.226934.0465-9.5515-8.1485
190.8063-1.45480.40664.0593-2.67793.35970.19120.1075-0.0233-0.51150.01150.25610.1012-0.2073-0.15220.1840.0207-0.03550.1815-0.01790.199418.8964-0.5232-27.0556
201.364-0.38060.45262.191-0.38162.7827-0.0501-0.04420.09890.18240.041-0.0617-0.0332-0.03150.00790.11460.0252-0.01770.1225-0.0150.136926.8499-11.8626-16.9697
211.61310.22810.98964.8-0.37427.50670.16350.0469-0.03920.1544-0.03820.53190.3292-0.9802-0.09590.18-0.04370.00520.23520.00170.196216.6748-20.0954-15.7399
221.2343-0.16070.23932.3009-0.57073.115-0.0729-0.09170.03570.05570.04170.1204-0.0706-0.16330.00650.13210.025-0.00210.1144-0.02970.140922.9267-9.4138-20.6189
234.38990.64760.55494.8943-0.34144.1299-0.10520.260.2692-0.1135-0.1563-0.6917-0.07040.58040.21370.14970.0338-0.02830.24320.02810.272838.8905-13.0476-18.915
244.49770.2339-0.01974.9402-0.45054.9714-0.0359-0.35210.03920.4228-0.04030.00490.0027-0.10740.05470.18390.0361-0.03270.17560.00380.127730.1003-17.0185-6.5518
258.9118-0.4338-0.85855.75262.55153.3290.22440.1951-0.417-0.3001-0.0677-0.44760.79430.52320.0730.34690.11310.00420.1938-0.00620.219332.5455-26.422-19.437
267.9908-0.04430.26988.3127-1.74765.3733-0.0919-0.8603-0.36280.62240.04220.18690.4368-0.134-0.10410.29740.0061-0.01750.26320.04940.238222.9334-25.1006-7.3437
272.12810.6749-1.55441.1679-1.91293.61670.05150.153-0.0806-0.5764-0.1408-0.4423-0.40150.63620.23110.6268-0.11890.21850.4048-0.07120.283842.4802-7.4792-51.4463
282.377-0.4941-1.59262.8095-1.66633.5225-0.24920.25560.1676-0.68930.29890.1345-0.0046-0.2727-0.13630.3061-0.0473-0.05110.2314-0.06340.192122.5037-18.3198-38.9348
292.25281.1082-0.87240.6526-1.02984.0535-0.13060.3818-0.159-0.6696-0.0248-0.0262-0.2780.06660.13920.4563-0.01610.02880.242-0.05140.194832.3288-6.4727-46.2817
301.4542-0.3027-0.16830.7388-2.32088.21920.13450.53040.1366-0.91610.0530.6117-0.3483-1.0185-0.23970.63620.1215-0.11970.48940.07880.373122.0309-0.244-52.6182
311.68450.0369-0.25790.0922-0.52164.9922-0.00360.3681-0.0781-0.60010.01710.0858-0.16910.0686-0.03310.37940.0008-0.00910.1993-0.04260.147128.7563-8.7757-43.5891
321.8094-0.7842-0.44631.93-0.183.6091-0.01550.4268-0.1064-0.72080.08090.18450.0886-0.3011-0.02650.4552-0.0355-0.03050.2348-0.02190.161425.5306-10.3071-45.5437
331.9844-0.0505-0.89190.2266-0.70022.97030.13080.34320.1621-0.56710.0044-0.4431-0.58530.3936-0.07910.5309-0.05380.14740.3071-0.02390.211840.5399-2.1707-46.6892
344.27311.90866.14513.07592.21568.9889-0.4546-0.10370.485-0.90840.0756-0.2275-1.00560.16070.32690.589-0.01640.04540.28740.04580.308334.40349.3123-43.348
355.2251.4601-4.81449.1029-1.95634.47990.84521.54111.0828-1.08270.2051-0.0984-0.8446-1.3326-1.06770.74420.0214-0.03990.46010.13080.371129.60615.7869-57.0812
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 8 )A-1 - 8
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 33 )A9 - 33
3X-RAY DIFFRACTION3chain 'A' and (resid 34 through 63 )A34 - 63
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 77 )A64 - 77
5X-RAY DIFFRACTION5chain 'A' and (resid 78 through 121 )A78 - 121
6X-RAY DIFFRACTION6chain 'A' and (resid 122 through 132 )A122 - 132
7X-RAY DIFFRACTION7chain 'A' and (resid 133 through 147 )A133 - 147
8X-RAY DIFFRACTION8chain 'A' and (resid 148 through 158 )A148 - 158
9X-RAY DIFFRACTION9chain 'A' and (resid 159 through 172 )A159 - 172
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 18 )B1 - 18
11X-RAY DIFFRACTION11chain 'B' and (resid 19 through 33 )B19 - 33
12X-RAY DIFFRACTION12chain 'B' and (resid 34 through 63 )B34 - 63
13X-RAY DIFFRACTION13chain 'B' and (resid 64 through 81 )B64 - 81
14X-RAY DIFFRACTION14chain 'B' and (resid 82 through 113 )B82 - 113
15X-RAY DIFFRACTION15chain 'B' and (resid 114 through 140 )B114 - 140
16X-RAY DIFFRACTION16chain 'B' and (resid 141 through 148 )B141 - 148
17X-RAY DIFFRACTION17chain 'B' and (resid 149 through 169 )B149 - 169
18X-RAY DIFFRACTION18chain 'C' and (resid 3 through 18 )C3 - 18
19X-RAY DIFFRACTION19chain 'C' and (resid 19 through 33 )C19 - 33
20X-RAY DIFFRACTION20chain 'C' and (resid 34 through 63 )C34 - 63
21X-RAY DIFFRACTION21chain 'C' and (resid 64 through 77 )C64 - 77
22X-RAY DIFFRACTION22chain 'C' and (resid 78 through 113 )C78 - 113
23X-RAY DIFFRACTION23chain 'C' and (resid 114 through 132 )C114 - 132
24X-RAY DIFFRACTION24chain 'C' and (resid 133 through 147 )C133 - 147
25X-RAY DIFFRACTION25chain 'C' and (resid 148 through 158 )C148 - 158
26X-RAY DIFFRACTION26chain 'C' and (resid 159 through 169 )C159 - 169
27X-RAY DIFFRACTION27chain 'D' and (resid 3 through 18 )D3 - 18
28X-RAY DIFFRACTION28chain 'D' and (resid 19 through 33 )D19 - 33
29X-RAY DIFFRACTION29chain 'D' and (resid 34 through 63 )D34 - 63
30X-RAY DIFFRACTION30chain 'D' and (resid 64 through 77 )D64 - 77
31X-RAY DIFFRACTION31chain 'D' and (resid 78 through 100 )D78 - 100
32X-RAY DIFFRACTION32chain 'D' and (resid 101 through 113 )D101 - 113
33X-RAY DIFFRACTION33chain 'D' and (resid 114 through 147 )D114 - 147
34X-RAY DIFFRACTION34chain 'D' and (resid 148 through 158 )D148 - 158
35X-RAY DIFFRACTION35chain 'D' and (resid 159 through 168 )D159 - 168

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