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- PDB-6eac: Pseudomonas syringae SelO -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6eac
TitlePseudomonas syringae SelO
ComponentsSelO
KeywordsTRANSFERASE / ampylation / selenoprotein / pseudokinase / flipped ATP / atypical kinase fold / adenylylation / oxidative stress / selenocysteine
Function / homology
Function and homology information


AMPylase activity / protein adenylyltransferase / magnesium ion binding / ATP binding
Similarity search - Function
Protein adenylyltransferase SelO / Protein adenylyltransferase SelO
Similarity search - Domain/homology
ACETATE ION / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DI(HYDROXYETHYL)ETHER / Protein adenylyltransferase SelO
Similarity search - Component
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.269 Å
AuthorsTomchick, D.R. / Tagliabracci, V.S. / Sreelatha, A.
Funding support United States, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R00DK099254 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094575 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115188 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)T32DK007257-37 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008203-29 United States
Robert A. Welch FoundationI-1911 United States
Robert A. Welch FoundationI-1505 United States
Robert A. Welch FoundationI-1561 United States
Other governmentRP170674 United States
CitationJournal: Cell / Year: 2018
Title: Protein AMPylation by an Evolutionarily Conserved Pseudokinase.
Authors: Sreelatha, A. / Yee, S.S. / Lopez, V.A. / Park, B.C. / Kinch, L.N. / Pilch, S. / Servage, K.A. / Zhang, J. / Jiou, J. / Karasiewicz-Urbanska, M. / Lobocka, M. / Grishin, N.V. / Orth, K. / ...Authors: Sreelatha, A. / Yee, S.S. / Lopez, V.A. / Park, B.C. / Kinch, L.N. / Pilch, S. / Servage, K.A. / Zhang, J. / Jiou, J. / Karasiewicz-Urbanska, M. / Lobocka, M. / Grishin, N.V. / Orth, K. / Kucharczyk, R. / Pawlowski, K. / Tomchick, D.R. / Tagliabracci, V.S.
History
DepositionAug 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _entity.formula_weight
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _entity.formula_weight
Revision 1.3Oct 31, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 4, 2020Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.6Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SelO
B: SelO
C: SelO
D: SelO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,33260
Polymers221,4374
Non-polymers4,89556
Water10,629590
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A: SelO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,86820
Polymers55,3591
Non-polymers1,50919
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SelO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,62316
Polymers55,3591
Non-polymers1,26415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SelO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,44112
Polymers55,3591
Non-polymers1,08211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SelO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,40012
Polymers55,3591
Non-polymers1,04111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.174, 158.056, 227.248
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
SelO


Mass: 55359.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Plasmid: ppSumo / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: Q87VB1, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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Non-polymers , 8 types, 646 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.017 M Tris-HCl, 0.2 M calcium acetate, 0.1 M sodium chloride, 1 mM TCEP, 1 mM AMP-PNP, 22% PEG 3350, 30% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97914 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2017 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.269→49.14 Å / Num. obs: 112381 / % possible obs: 99.5 % / Redundancy: 9.1 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.063 / Net I/σ(I): 11.5
Reflection shellResolution: 2.269→2.31 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5208 / Rpim(I) all: 0.292 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXmodel building
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.269→49.136 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.56
RfactorNum. reflection% reflection
Rfree0.2117 1999 1.82 %
Rwork0.1817 --
obs0.1822 110034 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 172.34 Å2 / Biso mean: 42.0551 Å2 / Biso min: 10.83 Å2
Refinement stepCycle: final / Resolution: 2.269→49.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15216 0 521 590 16327
Biso mean--55.42 32.81 -
Num. residues----1902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d015854
X-RAY DIFFRACTIONf_angle_d0.4921476
X-RAY DIFFRACTIONf_dihedral_angle_d10.89389
X-RAY DIFFRACTIONf_chiral_restr0.032264
X-RAY DIFFRACTIONf_plane_restr02826
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2689-2.32560.29481210.22046562668384
2.3256-2.38850.22941310.21757089722091
2.3885-2.45880.30751370.22057401753894
2.4588-2.53810.26461430.21377679782297
2.5381-2.62880.27141440.20777780792499
2.6288-2.73410.25181450.20757825797099
2.7341-2.85850.26331460.207579058051100
2.8585-3.00920.22811460.201978838029100
3.0092-3.19770.22091460.193178878033100
3.1977-3.44450.23481460.191279158061100
3.4445-3.79110.18111460.165179578103100
3.7911-4.33940.16331470.150479368083100
4.3394-5.4660.16781490.142280338182100
5.466-49.14750.18831520.18158183833599
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)
10.9077-0.6130.07361.1939-0.17430.59820.0161-0.10230.09210.15380.03070.2752-0.0571-0.0891-0.04930.2011-0.02090.01860.2774-0.02990.28810.547367.646363.9728
20.6098-0.2858-0.43560.96350.03830.8280.0029-0.0344-0.05580.0934-0.02430.2522-0.0495-0.14580.02410.20960.00260.00040.22010.00110.303212.391865.039860.0998
30.9899-0.07360.44680.7735-0.31770.89610.2439-0.1257-0.18060.1266-0.10030.12430.1839-0.113-0.09340.218-0.0026-0.0120.2048-0.01220.295318.326855.554959.8859
40.77810.1727-0.07350.3559-0.15850.94940.0123-0.0459-0.0089-0.0067-0.03340.036-0.02250.0556-0.00310.20750.013-0.03170.1809-0.02110.224516.913965.321351.3455
50.8766-0.22960.41610.5769-0.27590.7727-0.0250.105-0.11620.06890.0504-0.0579-0.03280.0326-0.01330.21410.0046-0.00730.2383-0.00740.246931.451460.648349.6702
61.17920.17760.85820.4569-0.11021.0960.0040.087-0.1251-0.08760.0292-0.10870.0120.1419-0.02660.21260.01040.02220.2525-0.04260.241342.091365.330147.961
70.7365-0.178-0.02582.11090.21850.82250.0409-0.1209-0.06570.1044-0.0723-0.33810.1530.20310.05320.22050.0304-0.05670.30020.01380.419760.591358.755459.0445
81.34810.6252-0.61261.1646-0.13280.59610.1123-0.0509-0.11970.1633-0.0415-0.07060.087-0.0072-0.0260.2426-0.0122-0.06360.2140.02680.241339.026459.819270.6436
90.70690.14970.1271.3159-0.20470.7328-0.01210.0763-0.0152-0.3503-0.01770.2360.1049-0.04820.02660.26630.0084-0.0620.21690.0090.280111.334716.308747.0324
100.4342-0.09380.37021.05330.04370.28830.0085-0.02020.0045-0.0268-0.02070.30430.01390.00150.00620.2271-0.00830.01690.23270.00650.326312.613718.529858.6748
110.97450.1697-0.11580.3612-0.22210.21140.05160.03910.0468-0.0346-0.04710.0899-0.06260.0193-0.02410.21590.00460.00620.1743-0.00990.281320.163325.859553.9128
120.7879-0.56780.00290.5408-0.06251.14710.0458-0.0149-0.05220.1243-0.01530.1809-0.00880.1325-0.03540.2283-0.03480.01950.2366-0.01630.259316.433718.072963.4887
130.9171-0.0279-0.45820.733-0.40530.843-0.01610.01770.1494-0.03930.0693-0.05820.0148-0.0094-0.03520.21540.0061-0.00570.2453-0.02680.259531.94422.610964.0831
140.98010.1614-0.54331.1769-0.08690.8049-0.0326-0.18510.03590.19270.0339-0.14620.0512-0.01670.00620.21290.0125-0.0420.2229-0.00890.1834.748215.083772.4118
151.2304-0.2525-0.19122.39720.40650.93230.0281-0.09870.46970.0326-0.0634-0.6434-0.08480.13170.01210.26170.01620.01830.2805-0.03910.503252.469321.628557.0518
160.8906-0.20820.50761.0575-0.26811.01550.01540.08110.39-0.1103-0.0249-0.5617-0.05010.1930.01520.25990.00410.07140.30070.00990.488751.393222.750750.0839
171.0596-0.58750.10711.4364-0.42241.20050.07940.45030.1838-0.4365-0.1281-0.1586-0.00390.02570.00330.3410.03240.06210.29020.06220.32234.743926.197639.3691
180.5602-0.1292-0.05930.78380.06430.9319-0.00060.0264-0.0655-0.1032-0.0632-0.07230.06720.0044-0.06520.28990.05520.04340.35270.01230.218511.220640.619595.9125
190.67150.329-0.15891.3764-0.59911.88710.01610.0180.0340.22470.0172-0.0554-0.5622-0.1143-0.04460.41930.10290.01890.3036-0.00120.23225.428668.894494.9285
200.6320.09950.37650.6643-0.07340.78210.0323-0.08620.00620.1003-0.01320.0215-0.1855-0.0062-0.00870.32090.0052-0.07540.3124-0.0250.25362.770451.302126.7268
210.53920.06830.16190.48640.15330.85430.01110.00560.0817-0.0314-0.01710.029-0.1721-0.0559-0.02230.35220.0017-0.09490.3086-0.02290.28864.752849.858922.6669
220.63280.47550.21030.35220.03040.6627-0.04580.04820.0818-0.04430.01640.0361-0.0926-0.11820.02870.3330.0083-0.08580.2948-0.00380.24533.555644.909214.4521
230.7411-0.0356-0.11440.94610.19471.23470.0055-0.2485-0.04020.3907-0.1836-0.4741-0.06350.45220.02740.3947-0.0748-0.13120.48350.00250.361927.594448.707224.329
240.61240.4651-0.03640.77970.21740.73850.00110.05660.05860.02620.0103-0.01850.10430.1528-0.02060.34210.0319-0.08350.3431-0.00340.295414.355132.539312.2083
250.88520.50350.24341.28830.20210.27220.08960.0524-0.1060.2-0.0559-0.32610.11880.3433-0.04040.31690.0427-0.06520.4106-0.00850.282825.790231.767113.5729
260.81530.0741-0.14411.2731-0.23771.91990.05410.1219-0.2199-0.2950.038-0.03630.52070.2259-0.04150.52360.046-0.11680.3469-0.03960.335313.11310.898715.7361
270.1480.2390.0680.70630.21872.15370.03010.1873-0.2388-0.15080.02230.04190.7194-0.0804-0.04770.71550.0634-0.08890.3212-0.06250.386610.88221.936214.1254
280.1918-0.0145-0.35951.26190.28640.99440.17050.1565-0.1573-0.0743-0.07880.04210.37580.0567-0.06290.3992-0.0134-0.08950.3024-0.03380.31743.105618.110122.5824
290.8725-0.5307-0.14161.5175-0.03920.73750.15150.0278-0.19460.07070.00290.25840.2482-0.125-0.09970.3743-0.0516-0.08480.3957-0.01360.3609-7.330625.116722.6982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 45 )A0 - 45
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 113 )A46 - 113
3X-RAY DIFFRACTION3chain 'A' and (resid 114 through 146 )A114 - 146
4X-RAY DIFFRACTION4chain 'A' and (resid 147 through 219 )A147 - 219
5X-RAY DIFFRACTION5chain 'A' and (resid 220 through 289 )A220 - 289
6X-RAY DIFFRACTION6chain 'A' and (resid 290 through 377 )A290 - 377
7X-RAY DIFFRACTION7chain 'A' and (resid 378 through 407 )A378 - 407
8X-RAY DIFFRACTION8chain 'A' and (resid 408 through 475 )A408 - 475
9X-RAY DIFFRACTION9chain 'B' and (resid 0 through 62 )B0 - 62
10X-RAY DIFFRACTION10chain 'B' and (resid 63 through 113 )B63 - 113
11X-RAY DIFFRACTION11chain 'B' and (resid 114 through 154 )B114 - 154
12X-RAY DIFFRACTION12chain 'B' and (resid 155 through 219 )B155 - 219
13X-RAY DIFFRACTION13chain 'B' and (resid 220 through 289 )B220 - 289
14X-RAY DIFFRACTION14chain 'B' and (resid 290 through 338 )B290 - 338
15X-RAY DIFFRACTION15chain 'B' and (resid 339 through 377 )B339 - 377
16X-RAY DIFFRACTION16chain 'B' and (resid 378 through 443 )B378 - 443
17X-RAY DIFFRACTION17chain 'B' and (resid 444 through 475 )B444 - 475
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 338 )C1 - 338
19X-RAY DIFFRACTION19chain 'C' and (resid 339 through 475 )C339 - 475
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 45 )D1 - 45
21X-RAY DIFFRACTION21chain 'D' and (resid 46 through 113 )D46 - 113
22X-RAY DIFFRACTION22chain 'D' and (resid 114 through 195 )D114 - 195
23X-RAY DIFFRACTION23chain 'D' and (resid 196 through 219 )D196 - 219
24X-RAY DIFFRACTION24chain 'D' and (resid 220 through 289 )D220 - 289
25X-RAY DIFFRACTION25chain 'D' and (resid 290 through 338 )D290 - 338
26X-RAY DIFFRACTION26chain 'D' and (resid 339 through 377 )D339 - 377
27X-RAY DIFFRACTION27chain 'D' and (resid 378 through 407 )D378 - 407
28X-RAY DIFFRACTION28chain 'D' and (resid 408 through 443 )D408 - 443
29X-RAY DIFFRACTION29chain 'D' and (resid 444 through 475 )D444 - 475

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