[English] 日本語
Yorodumi
- PDB-1va7: Yeast Myo3 SH3 domain, triclinic crystal form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1va7
TitleYeast Myo3 SH3 domain, triclinic crystal form
ComponentsMyosin-3 isoform
KeywordsCONTRACTILE PROTEIN / Structural genomics / SH3 domain
Function / homology
Function and homology information


bipolar cellular bud site selection / myosin I complex / actin cortical patch localization / positive regulation of Arp2/3 complex-mediated actin nucleation / fungal-type cell wall organization / cell tip / actin cortical patch / reticulophagy / response to osmotic stress / microfilament motor activity ...bipolar cellular bud site selection / myosin I complex / actin cortical patch localization / positive regulation of Arp2/3 complex-mediated actin nucleation / fungal-type cell wall organization / cell tip / actin cortical patch / reticulophagy / response to osmotic stress / microfilament motor activity / myosin binding / exocytosis / actin filament organization / cell periphery / endocytosis / actin filament binding / actin cytoskeleton / hydrolase activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Fungal myosin-I, SH3 domain / Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / SH3 Domains ...Fungal myosin-I, SH3 domain / Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / SH3 Domains / Kinesin motor domain superfamily / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKursula, P. / Lehmann, F. / Song, Y.H. / Wilmanns, M.
CitationJournal: To be Published
Title: High-throughput structural genomics of yeast SH3 domains
Authors: Kursula, P. / Lehmann, F. / Song, Y.H. / Wilmanns, M.
History
DepositionFeb 12, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 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 / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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: Myosin-3 isoform
B: Myosin-3 isoform
C: Myosin-3 isoform
D: Myosin-3 isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7666
Polymers30,5824
Non-polymers1842
Water00
1
A: Myosin-3 isoform


Theoretical massNumber of molelcules
Total (without water)7,6461
Polymers7,6461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myosin-3 isoform


Theoretical massNumber of molelcules
Total (without water)7,6461
Polymers7,6461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Myosin-3 isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7382
Polymers7,6461
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Myosin-3 isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7382
Polymers7,6461
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.800, 48.750, 48.840
Angle α, β, γ (deg.)60.70, 70.74, 70.60
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 1 / Auth seq-ID: 3 - 61 / Label seq-ID: 3 - 61

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
Detailseach chain is an independent biological unit

-
Components

#1: Protein
Myosin-3 isoform / Myo3


Mass: 7645.547 Da / Num. of mol.: 4 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / References: UniProt: P36006
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: sodium citrate, glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8115 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8115 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 6221 / Num. obs: 6221 / % possible obs: 96.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 33 Å2 / Rsym value: 0.106 / Net I/σ(I): 7.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 609 / Rsym value: 0.406 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RUW

1ruw


Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.846 / SU B: 24.02 / SU ML: 0.436 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS parameters used / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R Free: 0.484 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28017 311 5 %RANDOM
Rwork0.23625 ---
all0.23831 6220 --
obs0.23831 6220 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 6.195 Å2
Baniso -1Baniso -2Baniso -3
1--1.86 Å2-0.64 Å2-1.53 Å2
2---0.6 Å26.61 Å2
3----2.58 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 12 0 1994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222054
X-RAY DIFFRACTIONr_bond_other_d0.0020.021786
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.9852784
X-RAY DIFFRACTIONr_angle_other_deg0.78934222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8445252
X-RAY DIFFRACTIONr_chiral_restr0.0730.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022248
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02398
X-RAY DIFFRACTIONr_nbd_refined0.1780.2307
X-RAY DIFFRACTIONr_nbd_other0.2410.21795
X-RAY DIFFRACTIONr_nbtor_other0.0860.21149
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.223
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.26
X-RAY DIFFRACTIONr_mcbond_it0.1751.51280
X-RAY DIFFRACTIONr_mcangle_it0.28522060
X-RAY DIFFRACTIONr_scbond_it0.4083774
X-RAY DIFFRACTIONr_scangle_it0.5624.5724
Refine LS restraints NCS

Ens-ID: 1 / Number: 860 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
2Btight positional0.030.05
3Ctight positional0.030.05
4Dtight positional0.030.05
1Atight thermal0.050.5
2Btight thermal0.050.5
3Ctight thermal0.050.5
4Dtight thermal0.050.5
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.422 23
Rwork0.357 440
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)
18.4311-1.2325-0.74243.4952-0.53432.9893-0.3105-0.38920.3789-0.19550.3015-0.5001-0.12720.24810.0090.2812-0.0072-0.0340.2407-0.12050.23372.2494-0.62190.2925
211.986-0.32820.73861.3493-2.56872.4651-0.25890.3459-0.4322-0.03830.1702-0.37410.50620.36850.08870.4084-0.07980.02440.1738-0.19960.2414-17.161-8.19-13.0476
37.96962.27551.31162.8190.5799.1717-0.09070.0107-0.1716-0.7223-0.00220.3216-0.6493-0.36310.09290.4170.0151-0.04170.1349-0.04060.2569-29.51340.4357-28.4765
412.0048-2.7139-0.54515.53021.099710.41220.0045-0.08650.23851.00150.21580.26740.7593-0.6864-0.22030.4399-0.0636-0.00080.0766-0.03190.2228-10.2545-9.34515.6622
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 703 - 70
2X-RAY DIFFRACTION2BB3 - 703 - 70
3X-RAY DIFFRACTION3CC3 - 623 - 62
4X-RAY DIFFRACTION3CE71
5X-RAY DIFFRACTION4DD3 - 623 - 62
6X-RAY DIFFRACTION4DF71

+
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://pdbjlc1.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