[English] 日本語
Yorodumi
- PDB-6ah6: M500V mutant of Coronin coiled coil domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ah6
TitleM500V mutant of Coronin coiled coil domain
ComponentsCoronin-like protein
KeywordsSTRUCTURAL PROTEIN / Clash mutant(M500V) of Coronin Coiled Coil domain
Function / homology
Function and homology information


Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / Type of WD40 repeat / DUF1899 / DUF1900 / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / Type of WD40 repeat / DUF1899 / DUF1900 / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAnsari, A. / Karade, S.S. / Pratap, J.V.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research India
Citation
Journal: Int.J.Biol.Macromol. / Year: 2020
Title: Molecular and structural analysis of a mechanical transition of helices in the L. donovani coronin coiled-coil domain.
Authors: Karade, S.S. / Ansari, A. / Srivastava, V.K. / Nayak, A.R. / Pratap, J.V.
#1: Journal: J. Struct. Biol. / Year: 2016
Title: Structure of Leishmania donovani coronin coiled coil domain reveals an antiparallel 4 helix bundle with inherent asymmetry
Authors: Nayak, A.R. / Karade, S.S. / Pratap, J.V.
History
DepositionAug 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.3Nov 22, 2023Group: 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: Coronin-like protein
B: Coronin-like protein
C: Coronin-like protein
D: Coronin-like protein


Theoretical massNumber of molelcules
Total (without water)25,3494
Polymers25,3494
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-68 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.700, 49.830, 45.330
Angle α, β, γ (deg.)90.00, 112.51, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Coronin-like protein


Mass: 6337.237 Da / Num. of mol.: 4 / Mutation: M500V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Cell: Flagellar protein / Plasmid: pET-28a / Details (production host): T7-promoter, His tagg / Production host: Escherichia coli (E. coli) / Variant (production host): Rossetta pLysS / References: UniProt: Q3T1U8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.37 Å3/Da / Density % sol: 48.08 % / Description: shovel blade shaped
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Lithium sulfate, ammonium sulphate, sodium citrate 5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Sep 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→18.12 Å / Num. obs: 8088 / % possible obs: 94.67 % / Redundancy: 2 % / Biso Wilson estimate: 49.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.02494 / Rrim(I) all: 0.03527 / Net I/σ(I): 18.29
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 2 % / Rmerge(I) obs: 0.06221 / Mean I/σ(I) obs: 9.16 / Num. unique obs: 834 / CC1/2: 0.99 / Rrim(I) all: 0.08798 / % possible all: 99.88

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
iMOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER1.8.4_1496phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CX2

5cx2


Resolution: 2.5→18.12 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.73
RfactorNum. reflection% reflectionSelection details
Rfree0.2987 394 4.87 %5%
Rwork0.27 ---
obs-8082 95.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→18.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1391 0 0 28 1419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121393
X-RAY DIFFRACTIONf_angle_d1.3411886
X-RAY DIFFRACTIONf_dihedral_angle_d20.449495
X-RAY DIFFRACTIONf_chiral_restr0.09240
X-RAY DIFFRACTIONf_plane_restr0.007251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.5890.41171260.3262538X-RAY DIFFRACTION95
2.8606-3.59940.341220.30782586X-RAY DIFFRACTION96
3.5994-18.120.25481460.23132566X-RAY DIFFRACTION94
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)
17.9576-4.73552.24877.2353-0.41162.33250.5608-0.1799-0.1992-1.0976-0.12750.0830.1471-0.6984-0.37920.33090.00390.17430.4610.07460.308650.990838.13461.9957
23.3693-4.9062.76597.0798-3.33173.7559-0.07-0.38690.4614-0.00250.08-0.464-0.5588-0.2068-0.03410.40.04250.06870.4093-0.01760.351161.778734.96198.6598
34.665-3.93490.33934.699-0.98070.0626-0.1448-0.63140.58160.91280.246-0.4459-0.6324-0.8556-0.04520.70390.43950.34061.36830.00740.354652.939238.564215.4401
43.4536-0.57011.15960.9038-0.11760.28930.152-1.2551-1.020.2710.38010.3421-0.1328-0.8266-0.41530.58440.10930.20531.30940.38350.576455.931726.259117.5018
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 462 through 509 )
2X-RAY DIFFRACTION2chain 'B' and (resid 469 through 508 )
3X-RAY DIFFRACTION3chain 'C' and (resid 466 through 509 )
4X-RAY DIFFRACTION4chain 'D' and (resid 462 through 510 )

+
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