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- PDB-6plm: Legionella pneumophila SidJ/ Calmodulin 2 complex -

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Basic information

Entry
Database: PDB / ID: 6plm
TitleLegionella pneumophila SidJ/ Calmodulin 2 complex
Components
  • Calmodulin-2
  • SidJ protein
KeywordsTRANSFERASE / SidJ / Calmodulin / polyglutamylation / pseudokinase
Function / homology
Function and homology information


Ligases / negative regulation of calcium ion transmembrane transporter activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / protein phosphatase activator activity / ligase activity / positive regulation of phosphoprotein phosphatase activity ...Ligases / negative regulation of calcium ion transmembrane transporter activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / protein phosphatase activator activity / ligase activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / positive regulation of protein dephosphorylation / cysteine-type peptidase activity / regulation of calcium-mediated signaling / titin binding / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / positive regulation of protein serine/threonine kinase activity / spindle microtubule / spindle pole / response to calcium ion / G2/M transition of mitotic cell cycle / calcium-dependent protein binding / myelin sheath / transferase activity / vesicle / transmembrane transporter binding / G protein-coupled receptor signaling pathway / nucleotide binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / proteolysis / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm
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-2 / Calmodulin-dependent glutamylase SidJ
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.592 Å
AuthorsMao, Y. / Sulpizio, A. / Minelli, M.E. / Wu, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM094347 United States
CitationJournal: Elife / Year: 2019
Title: Protein polyglutamylation catalyzed by the bacterial calmodulin-dependent pseudokinase SidJ.
Authors: Sulpizio, A. / Minelli, M.E. / Wan, M. / Burrowes, P.D. / Wu, X. / Sanford, E.J. / Shin, J.H. / Williams, B.C. / Goldberg, M.L. / Smolka, M.B. / Mao, Y.
History
DepositionJul 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: SidJ protein
B: SidJ protein
C: Calmodulin-2
D: Calmodulin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,27314
Polymers207,9864
Non-polymers1,28710
Water2,810156
1
A: SidJ protein
C: Calmodulin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6377
Polymers103,9932
Non-polymers6435
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SidJ protein
D: Calmodulin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6377
Polymers103,9932
Non-polymers6435
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.351, 103.792, 110.194
Angle α, β, γ (deg.)90.00, 104.69, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 900
2114B1 - 900
1124C1 - 149
2124D1 - 149

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.295541, 0.14417, -0.944389), (0.15161, -0.983097, -0.102634), (-0.943223, -0.112847, -0.312403)78.07452, 34.41334, 111.94678

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein SidJ protein


Mass: 87487.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2155 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5ZTK6
#2: Protein Calmodulin-2


Mass: 16506.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM2, CAM2, CAMB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DP24

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Non-polymers , 4 types, 166 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris pH 9.2, 0.2 M Sodium Iodide , 15% PEG 3350, 1 mM Calcium Chloride, 1 mM ATP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.59→29.33 Å / Num. obs: 69809 / % possible obs: 97.7 % / Redundancy: 6.908 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 13.2
Reflection shellResolution: 2.59→2.66 Å / Rmerge(I) obs: 0.797 / Num. unique obs: 3687

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.592→29.33 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.24055 --
Rwork0.17573 --
obs-66333 97.69 %
Refinement stepCycle: LAST / Resolution: 2.592→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14434 0 70 156 14660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01414847
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713275
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.66420059
X-RAY DIFFRACTIONr_angle_other_deg1.0041.63731188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.56251776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6522.911821
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.682152694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4251587
X-RAY DIFFRACTIONr_chiral_restr0.0850.21911
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216487
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022763
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.33.9147128
X-RAY DIFFRACTIONr_mcbond_other2.33.9137127
X-RAY DIFFRACTIONr_mcangle_it3.6175.8658896
X-RAY DIFFRACTIONr_mcangle_other3.6175.8658897
X-RAY DIFFRACTIONr_scbond_it2.7754.1987719
X-RAY DIFFRACTIONr_scbond_other2.7754.1987720
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.376.18811164
X-RAY DIFFRACTIONr_long_range_B_refined6.41145.46416605
X-RAY DIFFRACTIONr_long_range_B_other6.4145.45116594
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A11742MEDIUM POSITIONAL0.390.5
1A11742MEDIUM THERMAL3.762
2C2026MEDIUM POSITIONAL0.60.5
2C2026MEDIUM THERMAL4.262
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)
10.85580.03550.2481.0933-0.68872.13980.022-0.00920.01820.00580.0890.17370.1161-0.1611-0.1110.0439-0.02120.04640.02430.00240.09518.02411.511744.2968
21.2479-0.29390.05460.78440.00720.9955-0.03880.07460.01330.0408-0.02640.005-0.00260.10260.06520.0851-0.04070.04170.0319-0.0120.025739.582420.002989.8044
33.24230.3978-0.9521.5174-0.49842.7195-0.0980.01540.13860.04830.13480.7487-0.2528-0.9315-0.03690.3755-0.1392-0.12820.92350.14510.8863-24.61626.922846.3456
44.62940.2303-1.22571.6606-0.94882.87390.0313-0.8679-0.37280.3495-0.00890.12110.31960.1289-0.02240.51050.02540.00410.3782-0.00690.151227.319318.8753120.476
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A98 - 1004
2X-RAY DIFFRACTION2B97 - 1004
3X-RAY DIFFRACTION3C1 - 201
4X-RAY DIFFRACTION4D1 - 201

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