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- PDB-4zj9: Small heat shock protein AgsA from Salmonella typhimurium: Alpha ... -

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Basic information

Entry
Database: PDB / ID: 4zj9
TitleSmall heat shock protein AgsA from Salmonella typhimurium: Alpha crystallin domain
ComponentsAggregation suppressing protein
KeywordsCHAPERONE / small heat shock protein / crystallin / dimer
Function / homology
Function and homology information


identical protein binding / cytoplasm
Similarity search - Function
Small heat shock protein IbpA/IbpB, ACD domain / 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
Aggregation suppressing protein / Molecular chaperone (Small heat shock protein)
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2212
Polymers17,1031
Non-polymers1181
Water50428
1
A: Aggregation suppressing protein
hetero molecules

A: Aggregation suppressing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4434
Polymers34,2062
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_467y-1,x+1,-z+21
Buried area2790 Å2
ΔGint-30 kcal/mol
Surface area11180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.090, 53.090, 81.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Aggregation suppressing protein


Mass: 17103.096 Da / Num. of mol.: 1 / Fragment: UNP residues 12-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: agsA / Plasmid: pRSET C / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: D1MC98, UniProt: Q8ZPY6*PLUS
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.69 Å3/Da / Density % sol: 27.04 % / Description: Tetragonal crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% Pentaerythritol propoxylate (5/4 PO/OH), 0.1M MES-NaOH, 20% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→34.12 Å / Num. obs: 8413 / % possible obs: 99.8 % / Redundancy: 13.8 % / Net I/σ(I): 22.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLM7.0.9data reduction
SCALAdata scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W1Z

3w1z


Resolution: 2→34.12 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.865 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25435 378 4.5 %RANDOM
Rwork0.21994 ---
obs0.22155 7995 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.336 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å20 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2→34.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms717 0 8 28 753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.019738
X-RAY DIFFRACTIONr_bond_other_d0.0010.02692
X-RAY DIFFRACTIONr_angle_refined_deg1.9911.961006
X-RAY DIFFRACTIONr_angle_other_deg0.87431589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.339592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.23326.36433
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11415120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.229151
X-RAY DIFFRACTIONr_chiral_restr0.120.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02834
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02157
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.9084.201371
X-RAY DIFFRACTIONr_mcbond_other5.8974.198370
X-RAY DIFFRACTIONr_mcangle_it9.1476.274462
X-RAY DIFFRACTIONr_mcangle_other9.1416.279463
X-RAY DIFFRACTIONr_scbond_it7.74.921367
X-RAY DIFFRACTIONr_scbond_other7.694.932368
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.4417.147545
X-RAY DIFFRACTIONr_long_range_B_refined15.50635.027768
X-RAY DIFFRACTIONr_long_range_B_other15.56834.847759
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 31 -
Rwork0.265 571 -
obs--100 %
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)
10.3429-0.3094-0.60740.4137-0.05363.8497-0.13520.00820.04990.1334-0.0536-0.09860.07540.18270.18880.1469-0.0326-0.02480.05830.01390.1059.682757.283796.3879
21.35170.2114-1.0742.52020.36331.02660.0560.1039-0.03390.1597-0.17040.1167-0.1353-0.20470.11440.31190.095-0.10840.23-0.11510.0744-0.905663.036297.3576
30.4545-0.38610.56561.2118-1.96993.22-0.2696-0.06690.04730.06780.3119-0.0293-0.0765-0.6752-0.04230.10790.0148-0.0510.3696-0.02970.0617-6.970864.904475.9112
42.3948-1.699-2.8941.63731.27524.90310.08730.44430.10310.04-0.2847-0.2588-0.2823-0.60260.19740.11840.0356-0.05110.10260.02170.1061.992566.532385.2965
523.84916.0719-18.408810.832-12.404914.21020.9119-0.51050.70660.6348-0.34670.4674-0.70610.4018-0.56520.24180.0651-0.02980.1007-0.10140.1102-1.173165.2795106.5264
63.78491.88952.90653.2963-2.19867.9470.3944-0.3123-0.06130.4276-0.21930.0388-0.1088-0.1222-0.17510.1224-0.03350.00340.0459-0.01990.03366.197960.2865107.8289
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 51
2X-RAY DIFFRACTION1A52 - 59
3X-RAY DIFFRACTION1A118 - 123
4X-RAY DIFFRACTION1A125 - 132
5X-RAY DIFFRACTION2A68 - 71
6X-RAY DIFFRACTION2A76 - 81
7X-RAY DIFFRACTION2A105 - 108
8X-RAY DIFFRACTION3A82 - 104
9X-RAY DIFFRACTION4A60 - 67
10X-RAY DIFFRACTION5A72 - 75
11X-RAY DIFFRACTION6A109 - 117

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