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- PDB-4wwm: X-ray crystal structure of Sulfolobus solfataricus Urm1 -

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Basic information

Entry
Database: PDB / ID: 4wwm
TitleX-ray crystal structure of Sulfolobus solfataricus Urm1
ComponentsUncharacterized protein
KeywordsSIGNALING PROTEIN / Ubiquitin-like / Modifier / Archaea
Function / homology
Function and homology information


tRNA thio-modification / cytoplasm
Similarity search - Function
Ubiquitin-related modifier 1 / Urm1 (Ubiquitin related modifier) / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBray, S.M. / Anjum, S.R. / Blackwood, J.K. / Kilkenny, M.L. / Coelho, M.A. / Foster, B.M. / Pellegrini, L. / Robinson, N.P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G0701443 United Kingdom
CitationJournal: Nat Commun / Year: 2015
Title: Involvement of a eukaryotic-like ubiquitin-related modifier in the proteasome pathway of the archaeon Sulfolobus acidocaldarius.
Authors: Anjum, R.S. / Bray, S.M. / Blackwood, J.K. / Kilkenny, M.L. / Coelho, M.A. / Foster, B.M. / Li, S. / Howard, J.A. / Pellegrini, L. / Albers, S.V. / Deery, M.J. / Robinson, N.P.
History
DepositionNov 11, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 2.0Sep 13, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _struct_site_gen.auth_seq_id
Revision 2.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6173
Polymers21,5212
Non-polymers961
Water1,60389
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8572
Polymers10,7611
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)10,7611
Polymers10,7611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.494, 65.192, 109.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 10760.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: 98/2 / Gene: Ssol_1261 / Production host: Escherichia coli (E. coli) / References: UniProt: D0KRX8
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 30% PEG 4000, 0.2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Mar 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→28 Å / Num. obs: 12034 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.71 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.0642 / Net I/σ(I): 27.26
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 8.55 % / Rmerge(I) obs: 0.3046 / Mean I/σ(I) obs: 6.05 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→28 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 574 4.77 %Random selection
Rwork0.1933 ---
obs0.1949 12034 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 0 5 89 1398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031357
X-RAY DIFFRACTIONf_angle_d0.6611835
X-RAY DIFFRACTIONf_dihedral_angle_d11.069543
X-RAY DIFFRACTIONf_chiral_restr0.029216
X-RAY DIFFRACTIONf_plane_restr0.003228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1968-2.41780.25431480.20842806X-RAY DIFFRACTION100
2.4178-2.76740.25331360.20662798X-RAY DIFFRACTION100
2.7674-3.48560.26361400.19452886X-RAY DIFFRACTION100
3.4856-28.00070.1941500.1842970X-RAY DIFFRACTION99
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)
13.5751-3.94964.37314.3927-4.86855.39750.2332-0.0167-0.5813-0.29750.15720.46160.2902-0.2594-0.23730.1402-0.0050.01010.1286-0.04670.1872-4.490910.0253-5.8693
23.84580.43910.04823.2957-1.13946.1717-0.0511-0.2823-0.0137-0.35470.0392-0.14980.23210.48630.02950.1650.01570.00630.1391-0.00250.1614.328910.73531.012
38.4987-0.66935.01154.8577-0.0723.83740.0189-0.6333-0.26670.35320.0699-0.05310.3499-0.4544-0.31210.0871-0.03540.0420.2247-0.03280.182-6.057813.4675-1.7387
44.13610.4208-3.75775.0008-2.23034.1042-0.00960.3690.52530.08910.27140.6067-1.019-0.3392-0.22140.27460.0174-0.01430.2734-0.01940.2938-6.73219.8132-14.6962
54.92911.4998-0.08785.27630.92082.7962-0.26660.43140.4778-0.00540.18040.1991-0.5852-0.1947-0.04040.18410.0031-0.03340.18450.00670.18250.040519.442-11.8753
63.8638-2.07242.44521.3849-2.23564.6716-0.1497-0.19271.33340.352-0.17010.4421-1.2451-0.5294-0.17080.36180.1102-0.10080.2208-0.07040.37026.531321.8928-4.1753
76.5923.4163-3.43856.3267-3.84292.73720.00180.83720.63210.0815-0.3306-0.6686-0.34860.7360.25930.222-0.0956-0.03910.39420.08760.392110.951118.6934-9.0295
84.4094-0.39942.28494.1461-3.25653.44670.10290.93060.7137-0.4091-0.0816-0.85580.14230.83230.32340.2811-0.07280.0690.5544-0.05430.349610.418415.7706-13.3065
97.6850.54243.72712.7672-1.47675.25170.06770.5768-0.1103-0.0927-0.1402-0.38590.27620.3322-0.01570.21690.06030.00070.2226-0.09820.27154.15316.9766-11.9054
102.5204-2.3706-1.23855.0589-2.81036.19780.26260.322-0.1402-0.6820.09940.20450.414-0.01030.44730.3068-0.01540.02140.2698-0.15810.1977-0.79355.7875-18.6749
115.08561.91590.48414.5127-4.23436.9077-0.29550.5312-0.2615-0.59380.00420.47830.2396-0.5258-0.28620.2431-0.0297-0.04870.2366-0.05580.2231-7.559813.1835-19.7036
123.9455-2.59880.45376.9366-0.69886.54790.1287-0.013-0.53760.4060.1691-0.51350.87090.633-0.06020.26370.0603-0.05510.1165-0.11830.23222.2045.6833-7.8762
135.2885-0.6917-0.126.5965-0.89857.9378-0.0576-0.00570.0333-0.55060.33850.1476-0.2571-0.0463-0.13440.2493-0.0895-0.03030.15830.09110.2383-5.869622.807-25.7018
144.48390.19860.59554.1493-1.884.90690.14040.56950.1433-0.57470.29910.54870.2535-0.6965-0.18160.3691-0.084-0.08520.40660.16160.3611-10.665625.7706-33.7058
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 7 )
2X-RAY DIFFRACTION2chain 'A' and (resid 8 through 14 )
3X-RAY DIFFRACTION3chain 'A' and (resid 15 through 20 )
4X-RAY DIFFRACTION4chain 'A' and (resid 21 through 25 )
5X-RAY DIFFRACTION5chain 'A' and (resid 26 through 33 )
6X-RAY DIFFRACTION6chain 'A' and (resid 34 through 38 )
7X-RAY DIFFRACTION7chain 'A' and (resid 39 through 43 )
8X-RAY DIFFRACTION8chain 'A' and (resid 44 through 48 )
9X-RAY DIFFRACTION9chain 'A' and (resid 49 through 55 )
10X-RAY DIFFRACTION10chain 'A' and (resid 56 through 63 )
11X-RAY DIFFRACTION11chain 'A' and (resid 64 through 72 )
12X-RAY DIFFRACTION12chain 'A' and (resid 73 through 80 )
13X-RAY DIFFRACTION13chain 'B' and (resid 2 through 25 )
14X-RAY DIFFRACTION14chain 'B' and (resid 26 through 79 )

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