[English] 日本語
Yorodumi
- PDB-3aab: Small heat shock protein hsp14.0 with the mutations of I120F and ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3aab
TitleSmall heat shock protein hsp14.0 with the mutations of I120F and I122F in the form I crystal
ComponentsPutative uncharacterized protein ST1653
KeywordsCHAPERONE / alpha-crystallin domain
Function / homology
Function and homology information


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
ISOPROPYL ALCOHOL / Small heat shock protein StHsp14.0
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.851 Å
AuthorsTakeda, K. / Hayashi, T. / Abe, T. / Hirano, Y. / Hanazono, Y. / Yohda, M. / Miki, K.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Dimer structure and conformational variability in the N-terminal region of an archaeal small heat shock protein, StHsp14.0
Authors: Takeda, K. / Hayashi, T. / Abe, T. / Hirano, Y. / Hanazono, Y. / Yohda, M. / Miki, K.
History
DepositionNov 13, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 7, 2011Group: Database references
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Putative uncharacterized protein ST1653
B: Putative uncharacterized protein ST1653
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6016
Polymers28,2652
Non-polymers3364
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-12 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.366, 61.096, 96.136
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-127-

HOH

21A-176-

HOH

31B-170-

HOH

-
Components

#1: Protein Putative uncharacterized protein ST1653 / small heat shock protein hsp14.0


Mass: 14132.262 Da / Num. of mol.: 2 / Mutation: I120F, I122F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Gene: ST1653 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q970D9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 41.35 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5% isopropanol, 10mM magnesium chloride, 50 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: May 21, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 20341 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 31.078 Å2 / Rsym value: 0.039 / Net I/σ(I): 37.1
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3 / Num. unique all: 1909 / Rsym value: 0.285 / % possible all: 92.3

-
Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.851→37.778 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.813 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1033 5.08 %RANDOM
Rwork0.228 19294 --
obs-20327 96.87 %-
Solvent computationBsol: 83.41 Å2 / ksol: 0.296 e/Å3
Displacement parametersBiso max: 32.43 Å2 / Biso mean: 10.718 Å2 / Biso min: 2.15 Å2
Baniso -1Baniso -2Baniso -3
1-20.656 Å20 Å20 Å2
2--28.73 Å20 Å2
3---23.091 Å2
Refinement stepCycle: LAST / Resolution: 1.851→37.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1679 0 22 224 1925
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.6281
X-RAY DIFFRACTIONf_bond_d0.0041
X-RAY DIFFRACTIONf_chiral_restr0.051
X-RAY DIFFRACTIONf_dihedral_angle_d10.3951
X-RAY DIFFRACTIONf_plane_restr0.0021
X-RAY DIFFRACTIONf_nbd_refined4.0961
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)
11.7239-0.46720.90550.7985-0.22454.0694-0.14360.22740.045-0.19390.16570.02890.1233-0.2045-0.0221-0.158-0.2717-0.076-0.2584-0.0715-0.0852-2.069412.8557-11.8674
21.0184-0.23110.33250.7568-0.00181.2279-0.06460.3410.1082-0.36370.03180.1984-0.0694-0.31080.03280.3096-0.2844-0.07090.43150.07780.0501-5.699214.0865-31.0828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA14 - 123
2X-RAY DIFFRACTION2chain BB9 - 114

+
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