[English] 日本語
Yorodumi
- PDB-5ypx: Crystal structure of calaxin with magnesium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ypx
TitleCrystal structure of calaxin with magnesium
ComponentsCalaxin
KeywordsMETAL BINDING PROTEIN / EF-hand / Calcium-binding protein / Neuronal calcium sensor / Calcium ion
Function / homology
Function and homology information


calcium-dependent outer dynein arm binding / cytoskeletal motor regulator activity / regulation of flagellated sperm motility / 9+2 motile cilium / dynein heavy chain binding / beta-tubulin binding / axoneme / cell chemotaxis / calcium ion binding
Similarity search - Function
Recoverin family / EF hand / 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
Biological speciesCiona intestinalis (vase tunicate)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsShojima, T. / Hou, F. / Takahashi, Y. / Okai, M. / Mizuno, K. / Inaba, K. / Miyakawa, T. / Tanokura, M.
CitationJournal: Sci Rep / Year: 2018
Title: Crystal structure of a Ca2+-dependent regulator of flagellar motility reveals the open-closed structural transition
Authors: Shojima, T. / Hou, F. / Takahashi, Y. / Matsumura, Y. / Okai, M. / Nakamura, A. / Mizuno, K. / Inaba, K. / Kojima, M. / Miyakawa, T. / Tanokura, M.
History
DepositionNov 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calaxin
B: Calaxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0797
Polymers51,9572
Non-polymers1225
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-33 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.258, 65.258, 113.203
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein Calaxin


Mass: 25978.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ciona intestinalis (vase tunicate) / Gene: CALX, calx / Production host: Escherichia coli (E. coli) / References: UniProt: Q8T893
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: magnesium chloride, ammonium sulfate, PEG 5000 MME, barium chloride

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.836
11-H, K, -L20.164
ReflectionResolution: 2.64→46.1 Å / Num. obs: 14030 / % possible obs: 100 % / Redundancy: 7.6 % / Net I/σ(I): 17.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→42.76 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.046 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.058 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21185 740 5.3 %RANDOM
Rwork0.16261 ---
obs0.16519 13256 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.832 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.64→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3036 0 5 21 3062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193087
X-RAY DIFFRACTIONr_bond_other_d0.0020.022975
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.984134
X-RAY DIFFRACTIONr_angle_other_deg1.03536893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7835365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67725.033153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.25615620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5571514
X-RAY DIFFRACTIONr_chiral_restr0.0950.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023373
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02673
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_it3.4674.3251472
X-RAY DIFFRACTIONr_mcbond_other3.4664.3231471
X-RAY DIFFRACTIONr_mcangle_it5.4066.4731833
X-RAY DIFFRACTIONr_mcangle_other5.4056.4751834
X-RAY DIFFRACTIONr_scbond_it4.2534.7541615
X-RAY DIFFRACTIONr_scbond_other4.2514.7551616
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7116.9452302
X-RAY DIFFRACTIONr_long_range_B_refined9.0433.5053584
X-RAY DIFFRACTIONr_long_range_B_other9.03833.523582
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.637→2.705 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 59 -
Rwork0.214 969 -
obs--99.52 %

+
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