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- PDB-7q68: Crystal structure of Chaetomium thermophilum wild-type Ahp1 -

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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-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 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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


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


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

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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

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: 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

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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

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