[English] 日本語
Yorodumi
- PDB-2cdt: alpha-SPECTRIN SH3 DOMAIN A56S MUTANT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2cdt
Titlealpha-SPECTRIN SH3 DOMAIN A56S MUTANT
ComponentsSPECTRIN ALPHA CHAIN
KeywordsSTRUCTURAL PROTEIN / SH3-DOMAIN / CYTOSKELETON / CALMODULIN-BINDING / ACTIN-BINDING
Function / homology
Function and homology information


costamere / actin filament capping / cortical actin cytoskeleton / cell projection / actin filament binding / cell junction / actin cytoskeleton organization / calmodulin binding / calcium ion binding / plasma membrane
Similarity search - Function
Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / SH3 Domains / SH3 domain ...Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / SH3 Domains / SH3 domain / EF-hand domain pair / EF-hand, calcium binding motif / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / EF-Hand 1, calcium-binding site / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Roll / Mainly Beta
Similarity search - Domain/homology
Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsCasares, S. / Camara-Artigas, A. / Vega, M.C. / Lopez-Mayorga, O. / Conejero-Lara, F.
Citation
Journal: Proteins: Struct., Funct., Bioinf. / Year: 2007
Title: Cooperative Propagation of Local Stability Changes from Low-Stability and High-Stability Regions in a SH3 Domain.
Authors: Casares, S. / Lopez-Mayorga, O. / Vega, M.C. / Camara-Artigas, A. / Conejero-Lara, F.
#1: Journal: Nature / Year: 1992
Title: Crystal Structure of a Src-Homology 3 (SH3) Domain
Authors: Musacchio, A. / Noble, M. / Pauptit, R. / Wierenga, R. / Saraste, M.
History
DepositionJan 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SPECTRIN ALPHA CHAIN


Theoretical massNumber of molelcules
Total (without water)7,2451
Polymers7,2451
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)33.628, 42.302, 49.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein SPECTRIN ALPHA CHAIN / SPECTRIN / NON-ERYTHROID ALPHA CHAIN / FODRIN ALPHA CHAIN


Mass: 7245.244 Da / Num. of mol.: 1 / Fragment: SH3-DOMAIN, RESIDUES 969-1025 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Tissue: BRAIN / Plasmid: PBAT4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07751
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 1019 TO SER

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 53.2 %
Crystal growpH: 6
Details: 1.1M AMMONIUM SULPHATE, 90MM SODIUM CITRATE/CITRIC ACID, PH 6.0, 90 MM BIS-TRIS PROPANE, 0.9MM EDTA, 0.9MM DTT, 0.9MM SODIUM AZIDE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 2000 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→15 Å / Num. obs: 2316 / % possible obs: 89.3 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.2
Reflection shellResolution: 2.45→2.6 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 3.6 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H1G

1h1g
PDB Unreleased entry


Resolution: 2.54→14.92 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.838 / Cross valid method: THROUGHOUT / ESU R: 0.743 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 104 4.5 %RANDOM
Rwork0.246 ---
obs0.248 2212 90.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20 Å2
2---0.48 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.54→14.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms448 0 0 18 466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022441
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.954581
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.522552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.25824.11817
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.891569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.046152
X-RAY DIFFRACTIONr_chiral_restr0.0850.262
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02317
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2950.2192
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2281
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.219
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.212
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_it0.7011.5271
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2862426
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5633170
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3694.5155
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.54→2.61 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.472 9
Rwork0.333 169

+
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