[English] 日本語
Yorodumi
- PDB-1ynz: SH3 domain of yeast Pin3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ynz
TitleSH3 domain of yeast Pin3
ComponentsPin3p
KeywordsPROTEIN BINDING / SH3 domain
Function / homology
Function and homology information


RHOV GTPase cycle / actin cortical patch / negative regulation of Arp2/3 complex-mediated actin nucleation / Antigen processing: Ubiquitination & Proteasome degradation / Neutrophil degranulation / nucleus / cytoplasm
Similarity search - Function
: / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
: / [PSI+] inducibility protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKursula, P. / Kursula, I. / Zou, P. / Lehmann, F. / Song, Y.H. / Wilmanns, M.
CitationJournal: To be Published
Title: Structural analysis of the yeast SH3 domain proteome
Authors: Kursula, P. / Kursula, I. / Zou, P. / Lehmann, F. / Song, Y.H. / Wilmanns, M.
History
DepositionJan 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pin3p


Theoretical massNumber of molelcules
Total (without water)6,5161
Polymers6,5161
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.550, 26.940, 23.770
Angle α, β, γ (deg.)90.00, 102.76, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Pin3p


Mass: 6516.325 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / Strain (production host): RIL / References: GenBank: 6325412, UniProt: Q06449*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.1 Å3/Da / Density % sol: 42 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9537 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 2805 / Num. obs: 2805 / % possible obs: 96.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 21.7 Å2 / Rsym value: 0.109 / Net I/σ(I): 10.1
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 347 / Rsym value: 0.307 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.87 / SU B: 6.762 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.389 / ESU R Free: 0.233 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24227 140 5 %RANDOM
Rwork0.2109 ---
all0.21235 2801 --
obs0.21235 2801 97.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.405 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.48 Å2
2--0.66 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms456 0 0 28 484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022469
X-RAY DIFFRACTIONr_bond_other_d0.0020.02405
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.984634
X-RAY DIFFRACTIONr_angle_other_deg0.8363956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.268556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70325.65223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5221577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg40.069151
X-RAY DIFFRACTIONr_chiral_restr0.080.262
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02525
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0291
X-RAY DIFFRACTIONr_nbd_refined0.1690.270
X-RAY DIFFRACTIONr_nbd_other0.2350.2467
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2212
X-RAY DIFFRACTIONr_nbtor_other0.0830.2262
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.25
X-RAY DIFFRACTIONr_mcbond_it1.1632367
X-RAY DIFFRACTIONr_mcbond_other0.1262117
X-RAY DIFFRACTIONr_mcangle_it1.3823453
X-RAY DIFFRACTIONr_scbond_it1.8014226
X-RAY DIFFRACTIONr_scangle_it2.6385181
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 11 -
Rwork0.244 202 -
obs--99.53 %

+
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