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

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Basic information

Entry
Database: PDB / ID: 3gla
TitleCrystal Structure of the hspA from Xanthomonas axonopodis
ComponentsLow molecular weight heat shock protein
KeywordsCHAPERONE / hspA / shp / shsp / Xanthomonas axonopodis / high resolution / 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
PHOSPHATE ION / Low molecular weight heat shock protein
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 Å
AuthorsHilario, E. / Medrano, F.J. / Bertolini, M.C.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and preliminary X-ray diffraction analysis of XAC1151, a small heat-shock protein from Xanthomonas axonopodis pv. citri belonging to the alpha-crystallin family
Authors: Hilario, E. / Teixeira, E.C. / Pedroso, G.A. / Bertolini, M.C. / Medrano, F.J.
History
DepositionMar 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8114
Polymers22,6212
Non-polymers1902
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-10 kcal/mol
Surface area10180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.674, 128.674, 55.251
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: 11310.709 Da / Num. of mol.: 2 / Fragment: UNP residues 40-139
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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 3.89 Å3/Da / Density % sol: 68.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1 M Tris HCl, 1.2 M (NH4)2HPO4, pH 7.4, 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
ReflectionResolution: 1.64→26.973 Å / Num. obs: 41715 / % possible obs: 100 % / Redundancy: 5.5 % / Rsym value: 0.051
Reflection shellResolution: 1.64→1.71 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.476

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 56.12 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å26.97 Å
Translation2.5 Å26.97 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GME

1gme


Resolution: 1.64→26.97 Å / Cor.coef. Fo:Fc: 0.966 / WRfactor Rwork: 0.187 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.898 / SU B: 1.219 / SU ML: 0.041 / SU R Cruickshank DPI: 0.071 / Isotropic thermal model: Isotropic / σ(F): 0 / ESU R: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflection
Rwork0.184 --
obs0.184 41710 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.29 Å2 / Biso mean: 25.833 Å2 / Biso min: 9.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å20 Å2
2--0.52 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.64→26.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1576 0 10 300 1886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.0221613
X-RAY DIFFRACTIONr_angle_refined_deg3.2211.9652172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3145194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.0422285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32715287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.451525
X-RAY DIFFRACTIONr_chiral_restr0.1970.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0211245
X-RAY DIFFRACTIONr_mcbond_it1.9621.5975
X-RAY DIFFRACTIONr_mcangle_it3.33421576
X-RAY DIFFRACTIONr_scbond_it5.0363638
X-RAY DIFFRACTIONr_scangle_it8.2794.5596
LS refinement shellResolution: 1.64→1.684 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.524 3081 -
obs--99.97 %

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