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- PDB-6oqq: Legionella pneumophila SidJ/Saccharomyces cerevisiae calmodulin c... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6oqq
TitleLegionella pneumophila SidJ/Saccharomyces cerevisiae calmodulin complex
Components
  • Calmodulin
  • Legionella pneumophila SidJ
KeywordsTRANSFERASE / polyglutamylation / pseudokinase / atypical kinase fold
Function / homology
Function and homology information


regulation of membrane tubulation / spindle pole body organization / cell budding / Ligases / myosin I complex / central plaque of spindle pole body / regulation of microtubule nucleation / cellular bud / positive regulation of Arp2/3 complex-mediated actin nucleation / myosin V complex ...regulation of membrane tubulation / spindle pole body organization / cell budding / Ligases / myosin I complex / central plaque of spindle pole body / regulation of microtubule nucleation / cellular bud / positive regulation of Arp2/3 complex-mediated actin nucleation / myosin V complex / karyogamy involved in conjugation with cellular fusion / vacuole fusion, non-autophagic / microautophagy / actin cortical patch / incipient cellular bud site / cellular bud tip / cellular bud neck / mating projection tip / vesicle transport along actin filament / phosphatidylinositol biosynthetic process / mitogen-activated protein kinase binding / ligase activity / enzyme regulator activity / cysteine-type peptidase activity / cytoskeleton organization / Neutrophil degranulation / receptor-mediated endocytosis / endocytosis / protein import into nucleus / calcium-dependent protein binding / transferase activity / nucleotide binding / calcium ion binding / proteolysis / metal ion binding
Similarity search - Function
EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / PYROPHOSPHATE 2- / Calmodulin / Calmodulin-dependent glutamylase SidJ
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.102 Å
AuthorsTomchick, D.R. / Tagliabracci, V.S. / Black, M. / Osinski, A.
Funding support United States, Poland, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008014-34 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)F30HL143859-01 United States
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)T32GM-7062-44 United States
Robert A. Welch FoundationI-1911 United States
Other governmentRP170674 United States
Polish National Science Centre2014/15/B/NZ1/03559 Poland
CitationJournal: Science / Year: 2019
Title: Bacterial pseudokinase catalyzes protein polyglutamylation to inhibit the SidE-family ubiquitin ligases.
Authors: Black, M.H. / Osinski, A. / Gradowski, M. / Servage, K.A. / Pawlowski, K. / Tomchick, D.R. / Tagliabracci, V.S.
History
DepositionApr 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 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.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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Legionella pneumophila SidJ
B: Calmodulin
C: Legionella pneumophila SidJ
D: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,37835
Polymers232,9734
Non-polymers2,40631
Water12,430690
1
A: Legionella pneumophila SidJ
B: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,79121
Polymers116,4862
Non-polymers1,30519
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-73 kcal/mol
Surface area37370 Å2
MethodPISA
2
C: Legionella pneumophila SidJ
D: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,58714
Polymers116,4862
Non-polymers1,10012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-56 kcal/mol
Surface area38190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.490, 104.749, 107.770
Angle α, β, γ (deg.)90.000, 103.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Legionella pneumophila SidJ


Mass: 100338.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: SidJ / Plasmid: ppSumo / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q5ZTK6
#2: Protein Calmodulin / / CaM


Mass: 16147.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CMD1, YBR109C, YBR0904 / Plasmid: ppSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: P06787

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Non-polymers , 7 types, 721 molecules

#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 690 / 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: 2.48 Å3/Da / Density % sol: 50.41 % / Mosaicity: 0.581 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M sodium malonate, 0.01 M sodium chloride, 0.001 M magnesium chloride, 0.001 mM calcium chloride, 0.001 M AMP-CPP, 16-17% PEG 3350, 35-40% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 15, 2018 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 130441 / % possible obs: 98.8 % / Redundancy: 11.5 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.021 / Rrim(I) all: 0.078 / Χ2: 0.939 / Net I/σ(I): 7.7 / Num. measured all: 1496151
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.144.80.81458070.7660.3770.9010.90888.8
2.14-2.185.30.76761640.7940.3460.8440.91693.2
2.18-2.225.70.67363140.8490.2950.7370.90696.3
2.22-2.268.10.65865030.8840.2280.6990.97799
2.26-2.3190.58265290.9230.1930.6150.94299.2
2.31-2.3710.80.54165420.9580.1660.5670.93999.9
2.37-2.4211.60.49466150.9690.1470.5160.94399.9
2.42-2.4912.40.44165780.9790.1280.460.944100
2.49-2.5612.70.37765810.9810.1080.3920.95399.9
2.56-2.6512.70.31165500.9880.0890.3230.96199.9
2.65-2.7413.30.25866090.990.0730.2690.99100
2.74-2.8513.10.20565960.9920.0580.2130.96699.8
2.85-2.9813.80.1665870.9950.0440.1660.971100
2.98-3.1413.50.12265640.9960.0340.1260.96199.9
3.14-3.3313.40.09666180.9960.0270.10.946100
3.33-3.5913.50.07766170.9970.0220.080.939100
3.59-3.9513.60.06666050.9970.0180.0680.93999.8
3.95-4.5213.70.05966570.9980.0170.0620.91100
4.52-5.713.50.05866310.9980.0160.060.85799.8
5.7-5013.40.05467740.9980.0160.0570.87799.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.102→46.83 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.81
RfactorNum. reflection% reflection
Rfree0.2336 1992 1.77 %
Rwork0.2021 --
obs0.2026 112310 84.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 171.17 Å2 / Biso mean: 50.1174 Å2 / Biso min: 6.15 Å2
Refinement stepCycle: final / Resolution: 2.102→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14189 0 240 690 15119
Biso mean--45.1 36.82 -
Num. residues----1755
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 (%)
2.1021-2.15460.2505500.21182703275329
2.1546-2.21290.2842660.22133499356538
2.2129-2.2780.2349790.22294841492052
2.278-2.35150.24081170.22556810692774
2.3515-2.43560.25321670.22378906907396
2.4356-2.53310.2691650.212591759340100
2.5331-2.64830.27561670.203392569423100
2.6483-2.7880.21141720.206992759447100
2.788-2.96260.24491710.214492419412100
2.9626-3.19130.24981670.213192719438100
3.1913-3.51240.23341670.203592909457100
3.5124-4.02040.21151690.184392829451100
4.0204-5.06430.20741660.174393289494100
5.0643-46.8420.2311690.209594419610100
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)
11.48690.06670.20081.0426-0.35850.94580.1352-0.2083-0.18030.1253-0.00820.02050.1151-0.05-0.06290.1434-0.0521-0.02030.0423-0.00440.2003-30.0366-24.79752.1113
20.42190.07410.13780.86480.14421.1869-0.03190.64230.1889-0.3307-0.0061-0.0730.01050.29030.00590.23450.0338-0.0030.45080.04610.1736-28.78-8.2946-34.4404
30.9791-0.12830.10641.1803-0.24311.02270.03930.19210.001-0.0067-0.0021-0.14080.01280.1240.00660.09270.00830.01530.0523-0.05330.1731-23.79-12.7146-13.4176
40.9379-0.03780.1491.1788-0.40770.99830.0697-0.177-0.1330.22420.00610.0413-0.011-0.1624-0.00250.1272-0.02340.04040.0536-0.01990.2076-38.6026-14.71-0.0003
53.2962-1.2933-0.79215.48230.85573.5551-0.00380.22560.2343-0.26990.0240.5696-0.3515-0.5117-0.03720.2356-0.0647-0.08050.27070.04450.4134-55.7323-18.8581-11.32
65.59610.7706-2.64313.1988-1.99344.3454-0.0442-0.1548-0.33660.1381-0.0578-0.06290.22850.00410.02880.3179-0.0755-0.06130.2873-0.0530.4119-46.2963-29.6508-16.7128
70.06460.38970.02023.05481.98514.952-0.06630.0615-0.206-0.29160.1794-0.28050.0650.1357-0.09590.2835-0.1912-0.03110.2821-0.02760.5319-56.8922-32.2349-9.9625
80.16350.42570.26651.10030.69070.4281-0.07390.2759-0.4477-0.1011-0.06420.3220.5562-0.4440.12480.6296-0.3404-0.10910.7679-0.08190.7848-61.3269-34.177-18.1823
97.35550.5645-2.04881.5901-0.92663.4378-0.02450.3265-0.1544-0.00570.01080.5604-0.0262-0.68860.04140.298-0.0588-0.12850.52030.00450.6724-62.0297-23.8588-17.0711
100.15430.12970.65130.63761.14953.91410.01620.1227-0.0474-0.1202-0.00050.30170.0923-0.36050.01250.3374-0.09730.17870.8921-0.02140.9439-72.7049-21.2958-0.5711
112.1597-0.0451-0.80.35220.57931.19740.0164-0.42520.17660.29010.00590.2299-0.2278-0.3112-0.09790.5462-0.05040.24330.6542-0.01010.8926-66.9884-13.09929.7327
120.1278-0.09990.09350.12580.03980.33030.02870.02910.0557-0.04420.04580.1013-0.0602-0.1228-0.02740.85810.2232-0.05820.9165-0.01641.1715-74.7093-9.60423.2593
130.9914-0.5460.31570.8786-0.11281.2818-0.1856-0.7260.21150.07530.19010.1165-0.052-0.4366-0.02340.17530.05770.03510.5193-0.07910.0767-15.25610.527631.4171
140.82620.35770.84021.41940.22121.03890.1468-0.4375-0.4985-0.12520.1026-0.6040.11890.3614-0.07470.14790.1712-0.33250.8690.01170.051230.0831-13.860239.8037
151.56350.0270.29281.2992-0.360.77490.032-0.2946-0.0364-0.10930.0908-0.17840.00230.097-0.09790.1736-0.0084-0.03440.1663-0.06420.13979.5514-6.646127.222
162.07560.09350.18230.77570.0051.53840.382-1.1453-0.98610.17040.08220.15330.189-0.25050.46580.1805-0.0641-0.0720.61820.3050.1292-6.1238-13.848539.3466
170.8113-0.33090.18691.0923-0.72480.93830.0059-0.4044-0.07960.3927-0.0151-0.04340.08110.0063-0.03690.520.0197-0.06041.3962-0.13020.3204-2.4634-9.15959.5758
182.946-0.127-1.38330.01280.05590.65530.152-0.10450.19690.0661-0.0389-0.0088-0.18570.0199-0.09070.57530.1885-0.02411.3431-0.25480.3832-1.03953.529458.4023
190.33680.5310.45050.83550.70860.60040.2003-0.05660.25480.3537-0.2622-0.0099-0.1609-0.30080.08821.08780.0247-0.13121.2197-0.14450.7391-3.48244.256672.2414
200.49140.69550.9110.98561.29921.74370.0155-0.52990.57050.52350.0052-0.3036-0.48530.3247-0.00621.0491-0.0228-0.28481.13360.01280.88768.80796.483265.636
210.57660.2852-0.47420.2402-0.23710.39590.0884-0.37840.07810.4774-0.17490.28840.107-0.03470.02740.81270.02630.20141.6196-0.02530.4896-14.0219-9.129470.8852
220.1248-0.1030.20340.6203-0.14860.3345-0.0642-0.1407-0.26650.1049-0.02860.14640.2154-0.05620.0621.0704-0.03350.19561.34470.16420.9384-20.5316-21.596260.8565
230.36960.23390.01350.15120.00410.00510.10880.0463-0.0435-0.15350.0097-0.075-0.13770.0852-0.07561.34760.04690.02681.31540.16911.036-19.9225-22.003773.557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 99 through 357 )A99 - 357
2X-RAY DIFFRACTION2chain 'A' and (resid 358 through 499 )A358 - 499
3X-RAY DIFFRACTION3chain 'A' and (resid 500 through 654 )A500 - 654
4X-RAY DIFFRACTION4chain 'A' and (resid 655 through 846 )A655 - 846
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 20 )B4 - 20
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 29 )B21 - 29
7X-RAY DIFFRACTION7chain 'B' and (resid 30 through 39 )B30 - 39
8X-RAY DIFFRACTION8chain 'B' and (resid 40 through 65 )B40 - 65
9X-RAY DIFFRACTION9chain 'B' and (resid 66 through 78 )B66 - 78
10X-RAY DIFFRACTION10chain 'B' and (resid 79 through 92 )B79 - 92
11X-RAY DIFFRACTION11chain 'B' and (resid 93 through 118 )B93 - 118
12X-RAY DIFFRACTION12chain 'B' and (resid 119 through 146 )B119 - 146
13X-RAY DIFFRACTION13chain 'C' and (resid 100 through 330 )C100 - 330
14X-RAY DIFFRACTION14chain 'C' and (resid 331 through 500 )C331 - 500
15X-RAY DIFFRACTION15chain 'C' and (resid 501 through 623 )C501 - 623
16X-RAY DIFFRACTION16chain 'C' and (resid 624 through 842 )C624 - 842
17X-RAY DIFFRACTION17chain 'D' and (resid 5 through 20 )D5 - 20
18X-RAY DIFFRACTION18chain 'D' and (resid 21 through 39 )D21 - 39
19X-RAY DIFFRACTION19chain 'D' and (resid 40 through 55 )D40 - 55
20X-RAY DIFFRACTION20chain 'D' and (resid 56 through 65 )D56 - 65
21X-RAY DIFFRACTION21chain 'D' and (resid 66 through 102 )D66 - 102
22X-RAY DIFFRACTION22chain 'D' and (resid 103 through 118 )D103 - 118
23X-RAY DIFFRACTION23chain 'D' and (resid 119 through 146 )D119 - 146

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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