[English] 日本語
Yorodumi
- PDB-5ojf: Crystal Structure of KLC2-TPR domain (fragment [A1-B6] -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ojf
TitleCrystal Structure of KLC2-TPR domain (fragment [A1-B6]
ComponentsKinesin light chain 2
KeywordsMOTOR PROTEIN / Kinesin1 / KLC2 / TPR domain
Function / homology
Function and homology information


lysosome localization / kinesin complex / microtubule / mitochondrion / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsNguyen, T.Q. / Chenon, M. / Vilela, F. / Velours, C. / Andreani, J. / Fernandez-Varela, P. / Llinas, P. / Menetrey, J.
CitationJournal: PLoS ONE / Year: 2017
Title: Structural plasticity of the N-terminal capping helix of the TPR domain of kinesin light chain.
Authors: Nguyen, T.Q. / Chenon, M. / Vilela, F. / Velours, C. / Aumont-Nicaise, M. / Andreani, J. / Varela, P.F. / Llinas, P. / Menetrey, J.
History
DepositionJul 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kinesin light chain 2
B: Kinesin light chain 2
C: Kinesin light chain 2


Theoretical massNumber of molelcules
Total (without water)106,4103
Polymers106,4103
Non-polymers00
Water0
1
A: Kinesin light chain 2


Theoretical massNumber of molelcules
Total (without water)35,4701
Polymers35,4701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin light chain 2


Theoretical massNumber of molelcules
Total (without water)35,4701
Polymers35,4701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kinesin light chain 2


Theoretical massNumber of molelcules
Total (without water)35,4701
Polymers35,4701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.620, 116.470, 108.110
Angle α, β, γ (deg.)90.00, 99.51, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Kinesin light chain 2 / Klc2 protein


Mass: 35470.137 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klc2, mCG_8395 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91YS4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 12 % PEG 3350, 0.5 M Phos. pH 7.5 Glycerol 25 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980097 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980097 Å / Relative weight: 1
ReflectionResolution: 3.4→48.14 Å / Num. obs: 16593 / % possible obs: 99.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 135.76 Å2 / Rrim(I) all: 0.236 / Net I/σ(I): 4.55
Reflection shellResolution: 3.4→3.59 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.08 / Rrim(I) all: 1.168 / % possible all: 95.7

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CEQ, 3NF1

3ceq

3nf1


Resolution: 3.4→20 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.885 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.529
RfactorNum. reflection% reflectionSelection details
Rfree0.264 819 4.99 %RANDOM
Rwork0.232 ---
obs0.234 16409 99.9 %-
Displacement parametersBiso mean: 127.81 Å2
Baniso -1Baniso -2Baniso -3
1-24.417 Å20 Å2-5.5685 Å2
2---26.7335 Å20 Å2
3---2.3165 Å2
Refine analyzeLuzzati coordinate error obs: 0.54 Å
Refinement stepCycle: 1 / Resolution: 3.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6255 0 0 0 6255
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016360HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.198583HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2313SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes177HARMONIC2
X-RAY DIFFRACTIONt_gen_planes912HARMONIC5
X-RAY DIFFRACTIONt_it6360HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.28
X-RAY DIFFRACTIONt_other_torsion24.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion810SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7260SEMIHARMONIC4
LS refinement shellResolution: 3.4→3.63 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.278 148 4.96 %
Rwork0.223 2836 -
all0.226 2984 -
obs--99.93 %
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)
15.61840.1536-4.35821.1395-0.53555.84530.017-0.76430.00160.1069-0.0792-0.40750.01880.9670.0622-0.0790.12720.1256-0.28760.2065-0.0318.10619.302914.6915
25.66780.667-3.79252.4313-0.9815.12570.1325-0.5920.26890.57350.16860.2427-0.70780.2915-0.30120.40220.03050.2957-0.5848-0.0626-0.0434-8.420533.799420.2958
35.7524-0.0724-3.57951.49440.61594.8965-0.2061-0.1682-0.8781-0.1258-0.2687-0.12690.6571-0.47070.47480.21880.15180.2268-0.30080.2765-0.002-17.6793-7.074634.5491
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

+
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