[English] 日本語
Yorodumi
- PDB-6plm: Legionella pneumophila SidJ/ Calmodulin 2 complex -

+
Open data


ID or keywords:

Loading...

-
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


protein-glutamic acid ligase activity, initiating / protein-glutamic acid ligase activity, elongating / Ligases / negative regulation of calcium ion transmembrane transporter activity / negative regulation of calcium ion export across plasma membrane / presynaptic endocytosis / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of ryanodine-sensitive calcium-release channel activity / calcineurin-mediated signaling ...protein-glutamic acid ligase activity, initiating / protein-glutamic acid ligase activity, elongating / Ligases / negative regulation of calcium ion transmembrane transporter activity / negative regulation of calcium ion export across plasma membrane / presynaptic endocytosis / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of ryanodine-sensitive calcium-release channel activity / calcineurin-mediated signaling / protein phosphatase activator activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / calcium channel inhibitor activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / titin binding / voltage-gated potassium channel complex / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / cysteine-type peptidase activity / adenylate cyclase activator activity / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / spindle microtubule / long-term synaptic potentiation / response to calcium ion / spindle pole / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / 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 / metal ion binding / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
EF-hand / : / Recoverin; domain 1 / 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 ...EF-hand / : / Recoverin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more