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- PDB-3q9q: HspB1 fragment second crystal form -

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Basic information

Entry
Database: PDB / ID: 3q9q
TitleHspB1 fragment second crystal form
ComponentsHeat shock protein beta-1
KeywordsCHAPERONE / Alpha-crystallin domain / Charcot-Marie-Tooth disease / neuronopathy / Ig-like fold / Stress response / intra-cellular chaperones / nucleus
Function / homology
Function and homology information


negative regulation of protein kinase C signaling / anterograde axonal protein transport / cornified envelope / regulation of canonical NF-kappaB signal transduction / positive regulation of endothelial cell chemotaxis / regulation of translational initiation / protein kinase C inhibitor activity / regulation of protein phosphorylation / cellular response to vascular endothelial growth factor stimulus / positive regulation of blood vessel endothelial cell migration ...negative regulation of protein kinase C signaling / anterograde axonal protein transport / cornified envelope / regulation of canonical NF-kappaB signal transduction / positive regulation of endothelial cell chemotaxis / regulation of translational initiation / protein kinase C inhibitor activity / regulation of protein phosphorylation / cellular response to vascular endothelial growth factor stimulus / positive regulation of blood vessel endothelial cell migration / response to unfolded protein / vascular endothelial growth factor receptor signaling pathway / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / : / axon cytoplasm / protein folding chaperone / protein kinase C binding / proteasome complex / positive regulation of interleukin-1 beta production / ubiquitin binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / MAPK6/MAPK4 signaling / VEGFA-VEGFR2 Pathway / response to virus / platelet aggregation / spindle / Z disc / positive regulation of angiogenesis / positive regulation of tumor necrosis factor production / unfolded protein binding / response to heat / protein refolding / RNA polymerase II-specific DNA-binding transcription factor binding / cytoskeleton / Extra-nuclear estrogen signaling / intracellular signal transduction / regulation of autophagy / focal adhesion / protein kinase binding / negative regulation of apoptotic process / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Heat shock protein beta-1, ACD domain / Alpha crystallin/Small heat shock protein, animal type / 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 beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBaranova, E.V. / Beelen, S. / Gusev, N.B. / Strelkov, S.V.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Three-Dimensional Structure of alpha-Crystallin Domain Dimers of Human Small Heat Shock Proteins HSPB1 and HSPB6
Authors: Baranova, E.V. / Weeks, S.D. / Beelen, S. / Bukach, O.V. / Gusev, N.B. / Strelkov, S.V.
History
DepositionJan 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein beta-1
B: Heat shock protein beta-1


Theoretical massNumber of molelcules
Total (without water)18,5792
Polymers18,5792
Non-polymers00
Water1,04558
1
A: Heat shock protein beta-1


Theoretical massNumber of molelcules
Total (without water)9,2891
Polymers9,2891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock protein beta-1


Theoretical massNumber of molelcules
Total (without water)9,2891
Polymers9,2891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.455, 74.455, 119.971
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLYSLYSchain A and (resseq 94:114 or resseq 116:126 or resseq 133:170 )AA94 - 1148 - 28
12GLYGLYALAALAchain A and (resseq 94:114 or resseq 116:126 or resseq 133:170 )AA116 - 12630 - 40
13TYRTYRPROPROchain A and (resseq 94:114 or resseq 116:126 or resseq 133:170 )AA133 - 17047 - 84
21ARGARGLYSLYSchain B and (resseq 94:114 or resseq 116:126 or resseq 133:170 )BB94 - 1148 - 28
22GLYGLYALAALAchain B and (resseq 94:114 or resseq 116:126 or resseq 133:170 )BB116 - 12630 - 40
23TYRTYRPROPROchain B and (resseq 94:114 or resseq 116:126 or resseq 133:170 )BB133 - 17047 - 84

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Components

#1: Protein Heat shock protein beta-1 / HspB1 / 28 kDa heat shock protein / Estrogen-regulated 24 kDa protein / Heat shock 27 kDa protein / ...HspB1 / 28 kDa heat shock protein / Estrogen-regulated 24 kDa protein / Heat shock 27 kDa protein / HSP 27 / Stress-responsive protein 27 / SRP27


Mass: 9289.354 Da / Num. of mol.: 2 / Fragment: residues 90-171 / Mutation: E125A, E126A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPB1 / Plasmid: pPEP-TEV / Production host: Escherichia coli (E. coli) / References: UniProt: P04792
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.2M ammonium sulfate, 0.2M di-ammonium tartrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 29, 2008
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.2→43.9 Å / Num. all: 13766 / Num. obs: 10572 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Rsym value: 0.072 / Net I/σ(I): 15.7
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 4 / Rsym value: 0.76 / % possible all: 90

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q9P

3q9p


Resolution: 2.2→39.99 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.02 / σ(F): 1.35 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3125 791 7.48 %random
Rwork0.2808 ---
obs0.2831 10572 99.91 %-
all-13766 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.6 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso max: 161.04 Å2 / Biso mean: 66.6043 Å2 / Biso min: 22.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.5561 Å20 Å20 Å2
2---0.5561 Å2-0 Å2
3---1.1122 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1143 0 0 58 1201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051184
X-RAY DIFFRACTIONf_angle_d1.0181618
X-RAY DIFFRACTIONf_chiral_restr0.081189
X-RAY DIFFRACTIONf_plane_restr0.006207
X-RAY DIFFRACTIONf_dihedral_angle_d17.612437
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A529X-RAY DIFFRACTIONPOSITIONAL0.049
12B529X-RAY DIFFRACTIONPOSITIONAL0.049
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2001-2.33790.34691340.310115571691
2.3379-2.51840.30961300.293915871717
2.5184-2.77180.37441300.295915971727
2.7718-3.17280.33641290.286316031732
3.1728-3.99680.25611230.265816561779
3.9968-39.99690.3151450.273517811926
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)
11.8172-1.07230.08441.49290.0941.4639-0.05130.07-0.0145-0.0255-0.04990.0585-0.0713-0.01390.09210.198-0.0589-0.01840.2220.03790.228422.57016.676814.7839
21.72-2.38651.037-0.314-0.82353.40080.47240.1459-0.4618-0.4661-0.3891-0.0265-1.28310.7991-0.12561.1362-0.3424-0.03140.4138-0.06770.390411.557719.905744.7233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA89 - 94
2X-RAY DIFFRACTION2chain BB94 - 1

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