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- PDB-4zja: Small heat shock protein AgsA from Salmonella typhimurium: C-term... -

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Basic information

Entry
Database: PDB / ID: 4zja
TitleSmall heat shock protein AgsA from Salmonella typhimurium: C-terminal truncated construct
ComponentsAggregation suppressing protein
KeywordsCHAPERONE / small heat shock protein / oligomer / crystallin
Function / homologySmall heat shock protein IbpA/IbpB, ACD domain / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / identical protein binding / Aggregation suppressing protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.101 Å
AuthorsMani, N. / Suguna, K.
CitationJournal: Sci Rep / Year: 2016
Title: Multiple oligomeric structures of a bacterial small heat shock protein
Authors: Mani, N. / Bhandari, S. / Moreno, R. / Hu, L. / Prasad, B.V. / Suguna, K.
History
DepositionApr 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aggregation suppressing protein
B: Aggregation suppressing protein


Theoretical massNumber of molelcules
Total (without water)33,3642
Polymers33,3642
Non-polymers00
Water0
1
A: Aggregation suppressing protein
B: Aggregation suppressing protein
x 12


Theoretical massNumber of molelcules
Total (without water)400,36324
Polymers400,36324
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area53740 Å2
ΔGint-239 kcal/mol
Surface area148000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.400, 126.400, 126.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Aggregation suppressing protein


Mass: 16681.801 Da / Num. of mol.: 2 / Fragment: UNP residues 1-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: agsA / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: D1MC98

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% Pentaerythritol propoxylate (5/4 PO/OH), 0.1M MES-NaOH, 30% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 4.1→63.2 Å / Num. obs: 2757 / % possible obs: 100 % / Redundancy: 10.6 % / Net I/σ(I): 14.8
Reflection shellResolution: 4.1→4.32 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.01037 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
MOSFLM7.0.9data reduction
SCALAdata scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZJ9

4zj9


Resolution: 4.101→44.689 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 49.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4127 121 4.4 %
Rwork0.3858 --
obs0.387 2750 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.101→44.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1599 0 0 0 1599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071631
X-RAY DIFFRACTIONf_angle_d1.5392226
X-RAY DIFFRACTIONf_dihedral_angle_d16.896576
X-RAY DIFFRACTIONf_chiral_restr0.052262
X-RAY DIFFRACTIONf_plane_restr0.009287
LS refinement shellResolution: 4.101→4.32 Å
RfactorNum. reflection% reflection
Rfree0.4127 121 -
Rwork0.3858 2629 -
obs--100 %

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