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- PDB-5j7n: Crystal structure of a small heat-shock protein from Xylella fast... -

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Basic information

Entry
Database: PDB / ID: 5j7n
TitleCrystal structure of a small heat-shock protein from Xylella fastidiosa reveals a distinct high order structure
ComponentsLow molecular weight heat shock protein
KeywordsCHAPERONE / Small heat shock protein / Xylella fastidiosa / alpha-crystallin domain / citrus variegated chlorosis
Function / homology
Function and homology information


: / 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
Low molecular weight heat shock protein
Similarity search - Component
Biological speciesXylella fastidiosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFonseca, E.M.B. / Scorsato, V. / dos Santos, C.A. / Tomazini Jr., A. / Aparicio, R. / Polikarpov, I.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystal structure of a small heat-shock protein from Xylella fastidiosa reveals a distinct high-order structure.
Authors: Fonseca, E.M. / Scorsato, V. / Dos Santos, M.L. / Junior, A.T. / Tada, S.F. / Dos Santos, C.A. / de Toledo, M.A. / de Souza, A.P. / Polikarpov, I. / Aparicio, R.
History
DepositionApr 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Low molecular weight heat shock protein


Theoretical massNumber of molelcules
Total (without water)17,8811
Polymers17,8811
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8220 Å2
2
A: Low molecular weight heat shock protein

A: Low molecular weight heat shock protein


Theoretical massNumber of molelcules
Total (without water)35,7622
Polymers35,7622
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area2920 Å2
ΔGint-3 kcal/mol
Surface area13530 Å2
MethodPISA
3
A: Low molecular weight heat shock protein

A: Low molecular weight heat shock protein


Theoretical massNumber of molelcules
Total (without water)35,7622
Polymers35,7622
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area2560 Å2
ΔGint-6 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.940, 68.940, 72.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Low molecular weight heat shock protein


Mass: 17880.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xylella fastidiosa (strain 9a5c) (bacteria)
Strain: 9a5c / Gene: XF_2234 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9PBB0

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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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES sodium salt pH 7.5, 0.3 M sodium citrate, 20% 2-propanol, 15% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.9→68.94 Å / Num. obs: 4089 / % possible obs: 98 % / Redundancy: 18.6 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 17.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 19.3 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 3.5 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
SCALAdata scaling
MOSFLMdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GLA

3gla


Resolution: 2.9→40.452 Å / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 20.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.23 183 4.48 %RANDOM
Rwork0.2122 ---
obs0.2131 4085 97.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→40.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms858 0 0 0 858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01876
X-RAY DIFFRACTIONf_angle_d1.2081184
X-RAY DIFFRACTIONf_dihedral_angle_d19.037536
X-RAY DIFFRACTIONf_chiral_restr0.061127
X-RAY DIFFRACTIONf_plane_restr0.009159
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)
17.9795-0.0775-1.78826.3860.49413.22370.047-0.880.00040.5123-0.2772-0.1859-0.1780.20820.33630.4138-0.0091-0.04380.60020.02420.62-12.2202-32.00143.0281
25.5135-0.253-1.4977.57070.58891.2302-0.1621-1.73090.06110.71370.08670.37350.1365-0.10790.0860.69450.0121-0.00171.3255-0.17270.98769.9688-27.010711.0236
36.58520.5931-0.53835.07760.76756.4767-0.2075-1.0555-0.3838-0.22720.11960.52560.22610.33810.20220.45460.0341-0.13270.6180.01810.7037-16.3793-33.93991.6667
42.41412.3619-1.50243.53130.19683.83030.39550.1209-0.60330.2201-0.53280.80590.5881-1.07440.30870.66030.0142-0.10160.8578-0.2931.0181-45.5415-39.923-6.9852
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 85 )
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 103 )
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 135 )
4X-RAY DIFFRACTION4chain 'A' and (resid 136 through 149 )

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