[English] 日本語
Yorodumi
- PDB-5f6t: Structure of calexcitin-Gd3+ complex. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f6t
TitleStructure of calexcitin-Gd3+ complex.
ComponentsCalexcitin
Keywordscalcium-binding protein / EF-hand Neuronal calcium signalling
Function / homology
Function and homology information


EF-hand / Recoverin; domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
GADOLINIUM ATOM / Calexcitin
Similarity search - Component
Biological speciesDoryteuthis pealeii (longfin inshore squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsChataigner, L. / Guo, J. / Erskine, P.T. / Coker, A.R. / Wood, S.P. / Cooper, J.B.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Binding of Gd(3+) to the neuronal signalling protein calexcitin identifies an exchangeable Ca(2+)-binding site.
Authors: Chataigner, L. / Guo, J. / Erskine, P.T. / Coker, A.R. / Wood, S.P. / Gombos, Z. / Cooper, J.B.
History
DepositionDec 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references / Structure summary
Revision 1.2Apr 13, 2016Group: Database references
Revision 1.3Jul 20, 2016Group: Database references
Revision 1.4Jan 10, 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: Calexcitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5384
Polymers22,3011
Non-polymers2373
Water54030
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-12 kcal/mol
Surface area9320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.020, 77.020, 29.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein Calexcitin /


Mass: 22301.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Doryteuthis pealeii (longfin inshore squid)
Gene: cex / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76764
#2: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Gd
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 38 % / Description: Plates.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M sodium acetate trihydrate, 0.1 M TRIS pH 8.5, 30 % PEG 4000.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.2→29.3 Å / Num. all: 9020 / Num. obs: 9020 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 66.2 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.5
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 6 % / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 1.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ccm

2ccm


Resolution: 2.201→27.353 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 44.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3044 870 5.13 %
Rwork0.215 --
obs0.2193 9020 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.5 Å2
Refinement stepCycle: LAST / Resolution: 2.201→27.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 3 30 1555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091596
X-RAY DIFFRACTIONf_angle_d1.0582131
X-RAY DIFFRACTIONf_dihedral_angle_d16.69577
X-RAY DIFFRACTIONf_chiral_restr0.04219
X-RAY DIFFRACTIONf_plane_restr0.004274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2006-2.33840.46751280.39622677X-RAY DIFFRACTION99
2.3384-2.51880.42181550.38452651X-RAY DIFFRACTION99
2.5188-2.77210.36751650.31972676X-RAY DIFFRACTION100
2.7721-3.17270.37011600.25792704X-RAY DIFFRACTION100
3.1727-3.99520.27651340.17962686X-RAY DIFFRACTION100
3.9952-27.35480.22451280.1412706X-RAY DIFFRACTION99
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)
14.6202-2.2682-1.09632.53020.85594.7411-0.6261-0.0716-1.0973-0.01991.30680.0297-0.05960.26890.35730.5043-0.10990.17570.929-0.56720.2958-9.03916.77619.1926
20.8671-0.0591.77532.23340.33493.64870.3396-0.65380.7073-0.007-0.08110.3011-0.3804-0.7045-0.27520.412-0.02830.28010.6531-0.25390.7467-28.102324.89427.4471
33.9868-0.33340.98174.9957-0.77034.80770.5883-0.1194-0.6322-0.0924-0.04680.69280.36950.1138-0.40860.3368-0.06610.07690.3864-0.17560.5254-22.384112.52953.1352
45.7007-0.5428-0.10241.8938-2.11316.4851-0.0036-0.3568-0.44280.11640.81580.51260.45580.9671-0.60430.3959-0.03360.14470.5086-0.19920.7343-17.819218.3235-4.9187
52.9774-0.89460.63911.97670.04513.15190.3528-0.10560.5384-0.05210.4058-0.3716-0.70710.7871-0.59260.5351-0.1760.31570.725-0.40180.9167-9.832329.9948-1.1894
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 98 )
4X-RAY DIFFRACTION4chain 'A' and (resid 99 through 118 )
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 189 )

+
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