[English] 日本語
Yorodumi
- PDB-7lsv: Non-kinase domain of Legionella effector protein kinase LegK2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lsv
TitleNon-kinase domain of Legionella effector protein kinase LegK2
ComponentsCalmodulin-dependent protein kinase
KeywordsPROTEIN BINDING / Bacterial effector / Legionella / kinase
Function / homologyCa2+/calmodulin-dependent protein kinase / calcium/calmodulin-dependent protein kinase activity / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / ATP binding / MALONATE ION / Calmodulin-dependent protein kinase
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.58 Å
AuthorsBeyrakhova, K.A. / van Straaten, K. / Cygler, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-48370 Canada
CitationJournal: To Be Published
Title: Non-kinase domain of Legionella effector protein kinase LegK2
Authors: Beyrakhova, K.A. / van Straaten, K. / Cygler, M.
History
DepositionFeb 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calmodulin-dependent protein kinase
B: Calmodulin-dependent protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3085
Polymers41,1602
Non-polymers1483
Water3,657203
1
A: Calmodulin-dependent protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6032
Polymers20,5801
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calmodulin-dependent protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7053
Polymers20,5801
Non-polymers1252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.310, 54.750, 71.650
Angle α, β, γ (deg.)90.000, 107.040, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Calmodulin-dependent protein kinase


Mass: 20580.193 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: legK2, lpg2137 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5ZTM4, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.67 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.4 M Malonate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.58→42.769 Å / Num. obs: 43414 / % possible obs: 98.4 % / Redundancy: 5.732 % / Biso Wilson estimate: 19.83 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.054 / Χ2: 0.96 / Net I/σ(I): 23.89 / Num. measured all: 248836 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.58-1.625.7490.9162.0618219326331690.7121.00997.1
1.62-1.675.7520.7942.3817658317430700.7580.87496.7
1.67-1.715.7310.6782.8217175304529970.8410.74798.4
1.71-1.775.7440.5663.4116808298529260.8730.62498
1.77-1.825.7460.4194.5916232290028250.9370.46297.4
1.82-1.895.7510.3165.8915913283427670.960.34897.6
1.89-1.965.7170.2297.9715139268326480.9770.25398.7
1.96-2.045.7480.15511.5814795260025740.990.17199
2.04-2.135.7420.10516.4414130249324610.9950.11698.7
2.13-2.235.7560.07821.3813545238523530.9970.08798.7
2.23-2.365.7440.05927.612895226822450.9980.06599
2.36-2.55.7410.04931.7912436218521660.9990.05499.1
2.5-2.675.7490.04136.311555202120100.9990.04699.5
2.67-2.885.7270.03343.2610830191418910.9990.03798.8
2.88-3.165.7610.02753.3298111712170310.0399.5
3.16-3.535.7330.0269.8390701585158210.02299.8
3.53-4.085.6980.01583.5779311400139210.01799.4
4.08-55.6990.01491.7668331203119910.01599.7
5-7.075.6020.01582.75515992292110.01699.9
7.07-42.7695.2470.01686.83270253051510.01897.2

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.58→42.769 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.205 2171 5 %
Rwork0.1771 41217 -
obs0.1785 43388 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.44 Å2 / Biso mean: 27.0045 Å2 / Biso min: 11.83 Å2
Refinement stepCycle: final / Resolution: 1.58→42.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2567 0 9 203 2779
Biso mean--68 32.28 -
Num. residues----315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092661
X-RAY DIFFRACTIONf_angle_d1.013590
X-RAY DIFFRACTIONf_chiral_restr0.06388
X-RAY DIFFRACTIONf_plane_restr0.007472
X-RAY DIFFRACTIONf_dihedral_angle_d11.6791633
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.58-1.61440.29041330.2675252497
1.6144-1.6520.30081330.2496252297
1.652-1.69330.24671340.2345254898
1.6933-1.73910.29391340.2347255297
1.7391-1.79020.24861340.2291254398
1.7902-1.8480.24611350.2091256598
1.848-1.91410.22691330.1938252098
1.9141-1.99070.21441350.184257298
1.9907-2.08130.21671350.1761256099
2.0813-2.1910.18021370.1657259999
2.191-2.32830.17681370.165259899
2.3283-2.5080.18311360.17259199
2.508-2.76040.20751370.1836259699
2.7604-3.15970.21171370.1847260799
3.1597-3.98050.18921390.1522651100
3.9805-42.7690.18731420.1574266999
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)
16.72040.58315.04712.13151.02514.336-0.24740.30690.4858-0.16060.0580.1394-0.73190.28150.22380.1873-0.0271-0.00430.1340.04430.2627-2.85845.81711.448
21.55190.3410.74431.31.15155.0246-0.00650.06610.1636-0.03880.1137-0.0359-0.26070.487-0.10530.1129-0.01270.00580.1923-0.01440.18133.64238.96414.487
32.8779-0.33190.49362.0721-1.10974.8760.0737-0.0869-0.14380.1169-0.0342-0.02750.02680.144-0.02880.08810.0106-0.00130.1295-0.01410.18387.56224.87720.111
42.13560.38360.67151.97921.29044.544-0.0440.26270.2836-0.25630.0648-0.0964-0.34320.28770.00050.1462-0.00860.01280.17450.04290.2103-7.32912.80446.963
52.2806-0.3130.07041.9256-1.5094.9290.03080.0184-0.096-0.0227-0.0192-0.03550.02730.0423-0.01370.06920.01120.00140.0892-0.02590.1853-2.995-3.6654.536
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 333:358 )A333 - 358
2X-RAY DIFFRACTION2( CHAIN A AND RESID 359:410 )A359 - 410
3X-RAY DIFFRACTION3( CHAIN A AND RESID 411:489 )A411 - 489
4X-RAY DIFFRACTION4( CHAIN B AND RESID 333:410 )B333 - 410
5X-RAY DIFFRACTION5( CHAIN B AND RESID 411:490 )B411 - 490

+
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://pdbjlvh1.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