[English] 日本語
Yorodumi
- PDB-2het: Non-myristoylated bovine recoverin (truncated at C-terminus) with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2het
TitleNon-myristoylated bovine recoverin (truncated at C-terminus) with calcium bound to EF-hand 3
ComponentsRecoverin
KeywordsMETAL BINDING PROTEIN / Recoverin / EF-hand / helix-loop-helix / calcium binding
Function / homology
Function and homology information


Inactivation, recovery and regulation of the phototransduction cascade / regulation of calcium ion transport / phototransduction / photoreceptor outer segment / regulation of signal transduction / photoreceptor inner segment / visual perception / perikaryon / calcium ion binding / membrane / cytosol
Similarity search - Function
Recoverin family / EF hand domain / EF-hand domain pair / EF-hand / Recoverin; domain 1 / 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. ...Recoverin family / EF hand domain / EF-hand domain pair / EF-hand / Recoverin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWeiergraber, O.H. / Granzin, J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Tuning of a neuronal calcium sensor.
Authors: Weiergraber, O.H. / Senin, I.I. / Zernii, E.Y. / Churumova, V.A. / Kovaleva, N.A. / Nazipova, A.A. / Permyakov, S.E. / Permyakov, E.A. / Philippov, P.P. / Granzin, J. / Koch, K.W.
History
DepositionJun 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Recoverin
B: Recoverin
C: Recoverin
D: Recoverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1548
Polymers86,9934
Non-polymers1604
Water00
1
A: Recoverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7882
Polymers21,7481
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Recoverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7882
Polymers21,7481
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Recoverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7882
Polymers21,7481
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Recoverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7882
Polymers21,7481
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-91 kcal/mol
Surface area31080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.889, 70.759, 85.925
Angle α, β, γ (deg.)90.00, 99.01, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Recoverin / p26


Mass: 21748.322 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: RCV1 / Plasmid: pET11d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P21457
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.4 M sodium malonate, 2 mM calcium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 25, 2006 / Details: Monochromators, mirrors
RadiationMonochromator: Diamond, germanium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3→70 Å / Num. all: 14380 / Num. obs: 14380 / % possible obs: 84.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 89.4 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 11.3
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2072 / Rsym value: 0.234 / % possible all: 84.1

-
Processing

Software
NameClassification
MOLREPphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OMR

1omr


Resolution: 3→70 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.259 775 Shells
Rwork0.237 --
all0.238 14370 -
obs0.238 14370 -
Displacement parametersBiso mean: 77.4 Å2
Baniso -1Baniso -2Baniso -3
1--10.64 Å20 Å24.03 Å2
2---8.18 Å20 Å2
3---18.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 3→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5756 0 4 0 5760
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.81

+
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