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- PDB-6yub: Crystal structure of Uba4 from Chaetomium thermophilum -

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Basic information

Entry
Database: PDB / ID: 6yub
TitleCrystal structure of Uba4 from Chaetomium thermophilum
Components(Adenylyltransferase and sulfurtransferase uba4) x 3
KeywordsTRANSFERASE / Ubiquitin-like protein activator 4
Function / homology
Function and homology information


molybdopterin synthase sulfurtransferase / URM1 activating enzyme activity / molybdopterin-synthase sulfurtransferase activity / molybdopterin-synthase adenylyltransferase / molybdopterin-synthase adenylyltransferase activity / protein urmylation / tRNA wobble position uridine thiolation / thiosulfate-cyanide sulfurtransferase activity / Mo-molybdopterin cofactor biosynthetic process / ATP binding ...molybdopterin synthase sulfurtransferase / URM1 activating enzyme activity / molybdopterin-synthase sulfurtransferase activity / molybdopterin-synthase adenylyltransferase / molybdopterin-synthase adenylyltransferase activity / protein urmylation / tRNA wobble position uridine thiolation / thiosulfate-cyanide sulfurtransferase activity / Mo-molybdopterin cofactor biosynthetic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
Adenylyltransferase and sulfurtransferase MOCS3/Uba4 / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Rhodanese-like domain / Rhodanese domain profile. ...Adenylyltransferase and sulfurtransferase MOCS3/Uba4 / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Adenylyltransferase and sulfurtransferase uba4
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.195 Å
AuthorsGrudnik, P. / Pabis, M. / Ethiraju Ravichandran, K. / Glatt, S.
Funding support Poland, 3items
OrganizationGrant numberCountry
Polish National Science Centre2018/31/B/NZ1/03559 Poland
Foundation for Polish ScienceFirstTEAM/2016-1/2 Poland
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6 Poland
CitationJournal: Embo J. / Year: 2020
Title: Molecular basis for the bifunctional Uba4-Urm1 sulfur-relay system in tRNA thiolation and ubiquitin-like conjugation.
Authors: Pabis, M. / Termathe, M. / Ravichandran, K.E. / Kienast, S.D. / Krutyholowa, R. / Sokolowski, M. / Jankowska, U. / Grudnik, P. / Leidel, S.A. / Glatt, S.
History
DepositionApr 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 14, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylyltransferase and sulfurtransferase uba4
B: Adenylyltransferase and sulfurtransferase uba4
C: Adenylyltransferase and sulfurtransferase uba4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4895
Polymers94,3583
Non-polymers1312
Water3,999222
1
A: Adenylyltransferase and sulfurtransferase uba4
B: Adenylyltransferase and sulfurtransferase uba4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3314
Polymers80,2002
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-38 kcal/mol
Surface area27360 Å2
MethodPISA
2
C: Adenylyltransferase and sulfurtransferase uba4


Theoretical massNumber of molelcules
Total (without water)14,1581
Polymers14,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.750, 74.170, 103.660
Angle α, β, γ (deg.)90.000, 106.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Adenylyltransferase and sulfurtransferase uba4


Mass: 47815.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: G0SC54
#2: Protein Adenylyltransferase and sulfurtransferase uba4


Mass: 32384.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: G0SC54
#3: Protein Adenylyltransferase and sulfurtransferase uba4


Mass: 14158.097 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: G0SC54
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 50 mM HEPES pH 6.9 and 23.5 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: May 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.195→47.63 Å / Num. obs: 48108 / % possible obs: 99.44 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rrim(I) all: 0.1412 / Net I/σ(I): 10.33
Reflection shellResolution: 2.195→2.274 Å / Mean I/σ(I) obs: 1.31 / Num. unique obs: 4560 / CC1/2: 0.689 / Rrim(I) all: 1.356

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1jw3

1jw3


Resolution: 2.195→47.628 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2526 2400 4.99 %
Rwork0.2081 45662 -
obs0.2103 48062 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 214.54 Å2 / Biso mean: 58.7014 Å2 / Biso min: 22.59 Å2
Refinement stepCycle: final / Resolution: 2.195→47.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6075 0 2 222 6299
Biso mean--41.72 52.22 -
Num. residues----824
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.195-2.23990.35961320.3382250593
2.2399-2.28860.37191400.3242264499
2.2886-2.34180.3311420.27382695100
2.3418-2.40040.30651410.25392700100
2.4004-2.46520.28021400.23832674100
2.4652-2.53780.25961410.22942662100
2.5378-2.61970.2821410.22862691100
2.6197-2.71330.28361420.23242703100
2.7133-2.82190.24781400.22392670100
2.8219-2.95040.27561430.23452710100
2.9504-3.10590.2621420.21092704100
3.1059-3.30040.23291420.2082685100
3.3004-3.55520.23291410.18852696100
3.5552-3.91280.18561430.17922704100
3.9128-4.47860.22161430.16862715100
4.4786-5.64110.24811400.18072712100
5.6411-47.6280.27251470.21522792100
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)
11.1003-0.63851.9140.8537-1.00184.801-0.1272-0.0021-0.12010.0383-0.0201-0.08930.17920.19350.17780.25590.00150.00880.30360.02230.5437-0.105814.28243.2765
24.1828-0.5371-0.5852.83210.58715.168-0.0875-0.3819-0.16460.34030.2738-0.44370.3840.846-0.11390.2950.0326-0.04550.2896-0.01790.487411.666114.144251.8726
32.5721.58552.97542.78823.91696.9654-0.06560.55930.1347-0.01370.296-0.47410.13560.8374-0.3350.29230.05940.04870.3962-0.00140.552611.873512.533733.3231
43.9938-2.5653-1.72315.4475-0.26541.4931-0.2073-0.21570.44180.39860.1225-0.78960.03660.10440.14490.313-0.09980.00760.3027-0.00550.553213.638537.831947.71
52.7495-0.1199-1.39266.43684.1663.36460.37350.21360.1979-0.67290.37350.3182-0.6136-1.3008-0.7560.8023-0.1188-0.05330.88820.20470.78395.416419.83810.8237
63.38173.5238-3.0819.0513-2.58142.8899-0.55530.51120.2384-0.7590.39560.36730.0892-0.66550.00271.03080.14090.04521.48730.48450.81346.564127.16-5.0545
76.9028-0.46664.76452.5701-0.84083.3268-0.22650.75960.4610.0468-0.1217-0.3661-0.61371.01050.35590.72210.01650.00740.85720.29410.618422.67221.4034.1472
82.3204-1.3419-0.49163.34030.75022.54110.04280.2811-0.2588-0.2478-0.2783-0.2874-0.0688-0.44510.27850.51640.14990.06270.91290.23280.596315.11925.10519.9349
94.77740.956-0.18416.72363.12287.6393-0.31221.0706-0.1795-0.4443-0.00380.64140.8749-0.26350.34710.7426-0.0763-0.05531.0860.19530.507811.760511.66421.841
102.23521.1052-1.70061.6969-0.34484.68010.05890.14180.0787-0.19380.04570.1968-0.10590.0539-0.16640.19820.0294-0.02260.26360.02780.3433-13.557711.412526.3407
112.4856-0.3685-0.06692.55760.22051.40980.00840.2462-0.2391-0.0066-0.01370.02450.157-0.0230.00960.2404-0.01190.01490.2605-0.0340.2788-12.9237-1.367727.8439
122.0616-0.5721-0.14212.64841.8162.8210.09060.4131-0.2457-0.13570.0468-0.02210.02490.1321-0.12730.2107-0.00920.00220.3905-0.03780.41120.5138-2.316422.8358
132.0161-0.1228-0.0520.334-0.23110.41610.00310.2916-0.2104-0.0394-0.0122-0.1847-0.01310.12230.02180.35270.0050.02120.3695-0.02960.470811.8175-2.4729.6151
144.06171.8171.49182.86050.88834.65150.00330.4884-0.5767-0.10510.047-0.53540.18640.2011-0.0040.32210.03170.05370.5391-0.0410.708228.08180.428817.0628
158.4385-3.8157-1.70583.3981-0.68156.06010.00360.5090.32870.27090.1844-0.0165-0.8589-0.5863-0.21270.37970.0383-0.05630.41210.1020.501125.938714.807627.6645
162.2389-1.52430.41282.2821-2.20113.44570.1022-0.5229-0.09580.17430.04070.2843-0.309-0.2643-0.03310.3533-0.03110.02430.3387-0.04490.4232-12.71877.827457.132
171.4857-0.0786-1.82587.4372-6.4439.7755-0.0228-0.025-0.15760.6892-0.30280.0821-0.45220.28940.15430.2438-0.01150.00940.2334-0.02290.3436-6.517417.314453.8748
180.86960.41760.46080.3160.06840.7935-0.09950.09730.2257-0.0728-0.0356-0.076-0.19790.02880.12780.2787-0.00390.02580.29410.02290.4338-11.199823.073936.908
192.37941.25410.27482.4690.16341.1493-0.0237-0.03680.1601-0.0925-0.0565-0.0393-0.07510.10230.07290.22860.03650.02660.22250.00550.3891-3.721827.978145.675
201.74381.1193.05333.84262.11265.2266-0.14910.21820.0832-0.1456-0.0088-0.284-0.22160.55880.11280.23980.00020.08320.3318-0.04380.475511.064122.63547.0177
213.52322.34982.67211.7131.97342.2273-0.00640.375-0.6173-0.12440.3136-0.3329-0.0990.1367-0.2820.3070.02760.08540.3931-0.04060.581613.591324.141844.3684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 209 through 229 )B209 - 229
2X-RAY DIFFRACTION2chain 'B' and (resid 230 through 256 )B230 - 256
3X-RAY DIFFRACTION3chain 'B' and (resid 257 through 277 )B257 - 277
4X-RAY DIFFRACTION4chain 'B' and (resid 278 through 304 )B278 - 304
5X-RAY DIFFRACTION5chain 'C' and (resid 318 through 330 )C318 - 330
6X-RAY DIFFRACTION6chain 'C' and (resid 331 through 337 )C331 - 337
7X-RAY DIFFRACTION7chain 'C' and (resid 338 through 392 )C338 - 392
8X-RAY DIFFRACTION8chain 'C' and (resid 393 through 422 )C393 - 422
9X-RAY DIFFRACTION9chain 'C' and (resid 423 through 444 )C423 - 444
10X-RAY DIFFRACTION10chain 'A' and (resid 3 through 89 )A3 - 89
11X-RAY DIFFRACTION11chain 'A' and (resid 90 through 168 )A90 - 168
12X-RAY DIFFRACTION12chain 'A' and (resid 169 through 242 )A169 - 242
13X-RAY DIFFRACTION13chain 'A' and (resid 243 through 350 )A243 - 350
14X-RAY DIFFRACTION14chain 'A' and (resid 351 through 422 )A351 - 422
15X-RAY DIFFRACTION15chain 'A' and (resid 423 through 444 )A423 - 444
16X-RAY DIFFRACTION16chain 'B' and (resid 2 through 25 )B2 - 25
17X-RAY DIFFRACTION17chain 'B' and (resid 26 through 44 )B26 - 44
18X-RAY DIFFRACTION18chain 'B' and (resid 45 through 89 )B45 - 89
19X-RAY DIFFRACTION19chain 'B' and (resid 90 through 159 )B90 - 159
20X-RAY DIFFRACTION20chain 'B' and (resid 160 through 178 )B160 - 178
21X-RAY DIFFRACTION21chain 'B' and (resid 179 through 208 )B179 - 208

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