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- PDB-2bol: CRYSTAL STRUCTURE AND ASSEMBLY OF TSP36, A METAZOAN SMALL HEAT SH... -

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Basic information

Entry
Database: PDB / ID: 2bol
TitleCRYSTAL STRUCTURE AND ASSEMBLY OF TSP36, A METAZOAN SMALL HEAT SHOCK PROTEIN
ComponentsSMALL HEAT SHOCK PROTEIN
KeywordsHEAT SHOCK PROTEIN / SMALL HEAT SHOCK PROTEIN / A-CRYSTALLIN / MOLECULAR CHAPERONE / TAENIA SAGINATA
Function / homology
Function and homology information


Arc Repressor Mutant, subunit A - #50 / Alpha crystallin/Small heat shock protein, animal type / Immunoglobulin-like - #790 / Arc Repressor Mutant, subunit A / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Helix non-globular / Special ...Arc Repressor Mutant, subunit A - #50 / Alpha crystallin/Small heat shock protein, animal type / Immunoglobulin-like - #790 / Arc Repressor Mutant, subunit A / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Helix non-globular / Special / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Small heat shock protein p36
Similarity search - Component
Biological speciesTAENIA SAGINATA (beef tapeworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsStamler, R.J. / Kappe, G. / Boelens, W.C. / Slingsby, C.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Wrapping the Alpha-Crystallin Domain Fold in a Chaperone Assembly.
Authors: Stamler, R.J. / Kappe, G. / Boelens, W.C. / Slingsby, C.
History
DepositionApr 12, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 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.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SMALL HEAT SHOCK PROTEIN
B: SMALL HEAT SHOCK PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4414
Polymers71,2492
Non-polymers1922
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.590, 102.050, 139.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999932, -0.011239, 0.003138), (0.010826, -0.793178, 0.608894), (-0.004354, 0.608886, 0.793246)
Vector: 174.4428, -1.514, 0.7045)

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Components

#1: Protein SMALL HEAT SHOCK PROTEIN / TSP36


Mass: 35624.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TAENIA SAGINATA (beef tapeworm) / Description: ONCOSPHERE / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7YZT0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52 %
Crystal growMethod: vapor diffusion, hanging drop
Details: HANGING DROP 1:1 PROTEIN:RESERVOIR SOLUTION 1.7 M AMMONIUM SULPHATE 10MM DTT 100 MM ADA (PH 6.5) 90 MM SODIUM POTASSIUM TARTRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97927
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 20, 2003 / Details: MIRRORS
RadiationMonochromator: SILICIUM / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.5→51.03 Å / Num. obs: 25578 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.5 / % possible all: 81.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→51.02 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1993606.46 / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH HENDRICKSON- - LATTMAN COEFFICIENTS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1317 5.1 %RANDOM
Rwork0.207 ---
obs0.207 25578 57 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 39.7426 Å2 / ksol: 0.373499 e/Å3
Displacement parametersBiso mean: 43.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--5.5 Å20 Å2
3----5.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.5→51.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4737 0 10 45 4792
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.261.5
X-RAY DIFFRACTIONc_mcangle_it7.052
X-RAY DIFFRACTIONc_scbond_it8.752
X-RAY DIFFRACTIONc_scangle_it11.172.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.363 134 5.1 %
Rwork0.269 2507 -
obs--47.7 %

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