[English] 日本語
Yorodumi
- PDB-3w1z: Heat shock protein 16.0 from Schizosaccharomyces pombe -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3w1z
TitleHeat shock protein 16.0 from Schizosaccharomyces pombe
ComponentsHeat shock protein 16
KeywordsCHAPERONE / alpha-crystallin domain / small heat shock protein
Function / homology
Function and homology information


protein aggregate center / cellular response to misfolded protein / protein complex oligomerization / cellular response to unfolded protein / response to salt stress / protein folding chaperone / response to hydrogen peroxide / unfolded protein binding / protein folding / cellular response to heat ...protein aggregate center / cellular response to misfolded protein / protein complex oligomerization / cellular response to unfolded protein / response to salt stress / protein folding chaperone / response to hydrogen peroxide / unfolded protein binding / protein folding / cellular response to heat / response to heat / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Immunoglobulin-like - #790 / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Heat shock protein 16
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsHanazono, Y. / Takeda, K. / Akiyama, N. / Aikawa, Y. / Miki, K.
CitationJournal: Structure / Year: 2013
Title: Nonequivalence Observed for the 16-Meric Structure of a Small Heat Shock Protein, SpHsp16.0, from Schizosaccharomyces pombe
Authors: Hanazono, Y. / Takeda, K. / Oka, T. / Abe, T. / Tomonari, T. / Akiyama, N. / Aikawa, Y. / Yohda, M. / Miki, K.
History
DepositionNov 26, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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: Heat shock protein 16
B: Heat shock protein 16
C: Heat shock protein 16
D: Heat shock protein 16


Theoretical massNumber of molelcules
Total (without water)63,9524
Polymers63,9524
Non-polymers00
Water1,67593
1
A: Heat shock protein 16
B: Heat shock protein 16
C: Heat shock protein 16
D: Heat shock protein 16

A: Heat shock protein 16
B: Heat shock protein 16
C: Heat shock protein 16
D: Heat shock protein 16

A: Heat shock protein 16
B: Heat shock protein 16
C: Heat shock protein 16
D: Heat shock protein 16

A: Heat shock protein 16
B: Heat shock protein 16
C: Heat shock protein 16
D: Heat shock protein 16


Theoretical massNumber of molelcules
Total (without water)255,80616
Polymers255,80616
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area63940 Å2
ΔGint-136 kcal/mol
Surface area93720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.296, 121.078, 122.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein
Heat shock protein 16 / 16 kDa heat shock protein


Mass: 15987.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / Gene: hsp16 / Production host: Escherichia coli (E. coli) / References: UniProt: O14368
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 15% PEGMME550, 100mM sodium chloride, 100mM Bicine buffer, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 22653 / % possible obs: 97.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 40.13 Å2 / Rsym value: 0.043 / Net I/σ(I): 21.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.254 / % possible all: 95.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GME

1gme


Resolution: 2.401→44.834 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.7417 / SU ML: 0.41 / σ(F): 0 / Phase error: 31.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 1154 5.1 %random
Rwork0.2457 ---
obs0.2478 22645 97.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.45 Å2 / Biso mean: 51.4625 Å2 / Biso min: 10.29 Å2
Refinement stepCycle: LAST / Resolution: 2.401→44.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4066 0 0 93 4159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054191
X-RAY DIFFRACTIONf_angle_d1.0495668
X-RAY DIFFRACTIONf_chiral_restr0.072643
X-RAY DIFFRACTIONf_plane_restr0.005749
X-RAY DIFFRACTIONf_dihedral_angle_d16.4661610
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4006-2.50980.40221580.33332567272595
2.5098-2.64220.351490.30922585273496
2.6422-2.80770.31091440.29072617276197
2.8077-3.02440.31311260.27152665279197
3.0244-3.32870.31271480.25082678282699
3.3287-3.81010.28861410.234927462887100
3.8101-4.79950.26051500.21692749289999
4.7995-44.84160.23811380.22422884302299

+
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