[English] 日本語
Yorodumi
- PDB-1shs: SMALL HEAT SHOCK PROTEIN FROM METHANOCOCCUS JANNASCHII -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1shs
TitleSMALL HEAT SHOCK PROTEIN FROM METHANOCOCCUS JANNASCHII
ComponentsSMALL HEAT SHOCK PROTEIN
KeywordsHEAT SHOCK PROTEIN / CHAPERONE / BETA-SANDWICH / Structural Genomics / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC
Function / homology
Function and homology information


protein folding chaperone / response to salt stress / response to hydrogen peroxide / : / unfolded protein binding / protein folding / protein complex oligomerization / response to heat / protein stabilization / protein-containing complex ...protein folding chaperone / response to salt stress / response to hydrogen peroxide / : / unfolded protein binding / protein folding / protein complex oligomerization / response to heat / protein stabilization / protein-containing complex / identical protein binding / 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
Small heat shock protein HSP16.5
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR, NCS AVERAGING / Resolution: 2.9 Å
AuthorsKim, K.K. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
Citation
Journal: Nature / Year: 1998
Title: Crystal structure of a small heat-shock protein.
Authors: Kim, K.K. / Kim, R. / Kim, S.H.
#1: Journal: J.Struct.Biol. / Year: 1998
Title: Purification, Crystallization, and Preliminary X-Ray Crystallographic Data Analysis of Small Heat Shock Protein Homolog from Methanococcus Jannaschii, a Hyperthermophile
Authors: Kim, K.K. / Yokota, H. / Santoso, S. / Lerner, D. / Kim, R. / Kim, S.H.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Small Heat Shock Protein of Methanococcus Jannaschii, a Hyperthermophile
Authors: Kim, R. / Kim, K.K. / Yokota, H. / Kim, S.H.
History
DepositionJul 30, 1998Processing site: BNL
Revision 1.0Jul 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SMALL HEAT SHOCK PROTEIN
B: SMALL HEAT SHOCK PROTEIN
C: SMALL HEAT SHOCK PROTEIN
D: SMALL HEAT SHOCK PROTEIN
E: SMALL HEAT SHOCK PROTEIN
F: SMALL HEAT SHOCK PROTEIN
G: SMALL HEAT SHOCK PROTEIN
H: SMALL HEAT SHOCK PROTEIN


Theoretical massNumber of molelcules
Total (without water)131,7608
Polymers131,7608
Non-polymers00
Water0
1
A: SMALL HEAT SHOCK PROTEIN
B: SMALL HEAT SHOCK PROTEIN
C: SMALL HEAT SHOCK PROTEIN
D: SMALL HEAT SHOCK PROTEIN
E: SMALL HEAT SHOCK PROTEIN
F: SMALL HEAT SHOCK PROTEIN
G: SMALL HEAT SHOCK PROTEIN
H: SMALL HEAT SHOCK PROTEIN

A: SMALL HEAT SHOCK PROTEIN
B: SMALL HEAT SHOCK PROTEIN
C: SMALL HEAT SHOCK PROTEIN
D: SMALL HEAT SHOCK PROTEIN
E: SMALL HEAT SHOCK PROTEIN
F: SMALL HEAT SHOCK PROTEIN
G: SMALL HEAT SHOCK PROTEIN
H: SMALL HEAT SHOCK PROTEIN

A: SMALL HEAT SHOCK PROTEIN
B: SMALL HEAT SHOCK PROTEIN
C: SMALL HEAT SHOCK PROTEIN
D: SMALL HEAT SHOCK PROTEIN
E: SMALL HEAT SHOCK PROTEIN
F: SMALL HEAT SHOCK PROTEIN
G: SMALL HEAT SHOCK PROTEIN
H: SMALL HEAT SHOCK PROTEIN


Theoretical massNumber of molelcules
Total (without water)395,28024
Polymers395,28024
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area80280 Å2
ΔGint-267 kcal/mol
Surface area109750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)171.440, 171.440, 101.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.041037, -0.427448, 0.903108), (0.735502, 0.624706, 0.262257), (-0.676279, 0.653475, 0.340025)-52.0428, -15.2007, 38.1647
2given(-0.843373, -0.537327, -0.001594), (-0.537313, 0.843367, -0.005267), (0.004174, -0.003585, -0.999985)0.4348, 0.3834, 116.2978
3given(-0.426968, 0.0241, -0.903946), (0.608952, 0.74666, -0.267725), (0.668487, -0.66477, -0.333475)52.5295, 15.5171, 78.1865
4given(0.036806, 0.737799, -0.674016), (-0.405421, 0.627498, 0.66474), (0.913389, 0.248794, 0.322215)38.6761, -38.5265, 39.9782
5given(-0.920358, 0.320555, 0.224023), (0.312979, 0.260264, 0.913404), (0.234491, 0.910773, -0.339862)-12.7644, -52.731, 77.9529
6given(-0.424174, 0.597454, 0.680533), (0.015745, 0.75624, -0.654105), (-0.905444, -0.26674, -0.330184)-39.3339, 38.1798, 77.3185
7given(0.354818, -0.906348, -0.229427), (0.24566, 0.327151, -0.912482), (0.902084, 0.267404, 0.338732)13.2155, 53.1379, 38.5867

-
Components

#1: Protein
SMALL HEAT SHOCK PROTEIN


Mass: 16469.990 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: PET21A-PSJS1240 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q57733

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 5.7 / Details: pH 5.7
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Kim, K.K., (1998) J.Struct.Biol., 121, 76. / PH range low: 5.7 / PH range high: 5.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
20.2-0.3 Msodium acetate1drop
325-30 %MPD1drop
40.02 M1dropCaCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95
DetectorType: BRANDEIS / Detector: CCD / Date: Nov 1, 1997
Details: ALUMINUM ELECTROLESS NICKEL-PLATED RHODIUM-COATED CYLINDRICAL 1:1 FOCUSING MIRROR
RadiationMonochromator: SINGLE FLAT CRYSTAL MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. obs: 24757 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 97.8 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 22.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 5.9 / Rsym value: 0.431 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
X-PLOR3.85model building
X-PLOR3.85refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.85phasing
RefinementMethod to determine structure: SIR, NCS AVERAGING / Resolution: 2.9→15 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2202 10 %RANDOM
Rwork0.216 ---
obs0.216 22008 89.6 %-
Displacement parametersBiso mean: 59.2 Å2
Baniso -1Baniso -2Baniso -3
1-22.551 Å211.199 Å20 Å2
2--22.551 Å20 Å2
3---23.02 Å2
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7144 0 0 0 7144
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.505
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d32.03
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.713
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.361.5
X-RAY DIFFRACTIONx_mcangle_it3.9442
X-RAY DIFFRACTIONx_scbond_it3.712
X-RAY DIFFRACTIONx_scangle_it5.9952.5
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev Biso : 3.427 Å2 / Rms dev position: 0.041 Å / Weight Biso : 2 / Weight position: 300
LS refinement shellResolution: 2.9→3.03 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3496 190 6.26 %
Rwork0.3503 1775 -
obs--64.78 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.85 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg32.03
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.713

+
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