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- PDB-3gt6: Crystal Structure of the hspA from Xanthomonas axonopodis -

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Basic information

Entry
Database: PDB / ID: 3gt6
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
Low molecular weight heat shock protein
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 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 27, 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

Downloads & links

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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
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint1 kcal/mol
Surface area10560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.590, 128.590, 55.290
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.: 148 / 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: 3.79 Å3/Da / Density % sol: 67.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 24% (w/v) PEG 1500, 20 % glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293 K

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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: 2.15→26.96 Å / Num. obs: 18680 / Redundancy: 3.8 % / Rmerge(I) obs: 0.049

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 28.34 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å26.96 Å
Translation2.5 Å26.96 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: 3GLA

3gla


Resolution: 2.15→26.96 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.196 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.855 / SU B: 3.865 / SU ML: 0.103 / SU R Cruickshank DPI: 0.175 / SU Rfree: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 955 5.1 %RANDOM
Rwork0.199 ---
obs0.201 18674 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: 60.93 Å2 / Biso mean: 26.304 Å2 / Biso min: 10.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.15→26.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1594 0 0 148 1742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221630
X-RAY DIFFRACTIONr_angle_refined_deg2.1691.962196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4995198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3812285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64715288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1681525
X-RAY DIFFRACTIONr_chiral_restr0.1390.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211265
X-RAY DIFFRACTIONr_mcbond_it1.3741.5996
X-RAY DIFFRACTIONr_mcangle_it2.53421610
X-RAY DIFFRACTIONr_scbond_it3.7583634
X-RAY DIFFRACTIONr_scangle_it6.2864.5586
LS refinement shellResolution: 2.15→2.201 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 75 -
Rwork0.245 1303 -
all-1378 -
obs--100 %

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