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- PDB-3guf: Crystal Structure of the hspA from Xanthomonas axonopodis -

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Basic information

Entry
Database: PDB / ID: 3guf
TitleCrystal Structure of the hspA from Xanthomonas axonopodis
ComponentsLow molecular weight heat shock protein
KeywordsCHAPERONE / hspA / shp / shsp / Xanthomonas axonopodis / small heat shock protein / citrus canker / Stress response
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 speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 Å
AuthorsHilario, E. / Medrano, F.J. / Bertolini, M.C.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal structures of Xanthomonas small heat shock protein provide a structural basis for an active molecular chaperone oligomer.
Authors: Hilario, E. / Martin, F.J. / Bertolini, M.C. / Fan, L.
History
DepositionMar 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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
B: Low molecular weight heat shock protein


Theoretical massNumber of molelcules
Total (without water)23,2202
Polymers23,2202
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-4 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.579, 110.579, 55.188
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Low molecular weight heat shock protein


Mass: 11610.074 Da / Num. of mol.: 2 / Fragment: UNP residues 37-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Gene: hspA / Plasmid: pET28a-hspA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8PNC2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 24 % (w/v) PEG 1500, 20 % glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.43 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.43 Å / Relative weight: 1
ReflectionRedundancy: 2.8 % / Av σ(I) over netI: 15.2 / Number: 32193 / Rsym value: 0.034 / D res high: 2.278 Å / D res low: 55.289 Å / Num. obs: 11413 / % possible obs: 96.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
7.1436.1798.710.0220.0222.9
5.057.1410010.0210.0212.9
4.125.0510010.0190.0192.9
3.574.1210010.0310.0312.9
3.193.5710010.0310.0312.9
2.913.1910010.0480.0482.8
2.72.9199.910.0720.0722.8
2.522.799.810.1140.1142.8
2.382.5299.410.1790.1792.8
2.262.3876.210.2680.2682.6
ReflectionResolution: 2.25→50 Å / Num. obs: 11451 / Redundancy: 2.8 %

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 28.28 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å36.17 Å
Translation2.5 Å36.17 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GLA

3gla


Resolution: 2.28→30.27 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.282 / WRfactor Rwork: 0.238 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.784 / SU B: 7.271 / SU ML: 0.184 / SU R Cruickshank DPI: 0.335 / SU Rfree: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.335 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.289 547 4.8 %RANDOM
Rwork0.239 ---
obs0.241 11409 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 83.74 Å2 / Biso mean: 43.018 Å2 / Biso min: 11.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.28→30.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1575 0 0 35 1610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221604
X-RAY DIFFRACTIONr_angle_refined_deg2.091.9592160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8835195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78122.14384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.40815284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9711524
X-RAY DIFFRACTIONr_chiral_restr0.1260.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211244
X-RAY DIFFRACTIONr_mcbond_it1.2581.5980
X-RAY DIFFRACTIONr_mcangle_it2.31121581
X-RAY DIFFRACTIONr_scbond_it3.1583624
X-RAY DIFFRACTIONr_scangle_it5.2784.5579
LS refinement shellResolution: 2.28→2.338 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 43 -
Rwork0.423 737 -
all-780 -
obs--92.09 %

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