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- PDB-3mii: Crystal structure of Y0R391Cp/HSP33 from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 3mii
TitleCrystal structure of Y0R391Cp/HSP33 from Saccharomyces cerevisiae
ComponentsProbable chaperone protein HSP33
KeywordsHYDROLASE / heat shock protein
Function / homology
Function and homology information


D-lactate dehydratase / glyoxalase III activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / cellular response to nutrient levels / chaperone-mediated protein folding / protein folding chaperone / P-body / cytoplasm
Similarity search - Function
Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Probable glutathione-independent glyoxalase HSP33
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGuo, P.-C. / Zhou, Y.-Y. / Zhou, C.-Z. / Li, W.-F.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of Hsp33/YOR391Cp from the yeast Saccharomyces cerevisiae
Authors: Guo, P.-C. / Zhou, Y.-Y. / Ma, X.-X. / Li, W.-F.
History
DepositionApr 10, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable chaperone protein HSP33
B: Probable chaperone protein HSP33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4746
Polymers53,9852
Non-polymers4894
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Probable chaperone protein HSP33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1432
Polymers26,9931
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Probable chaperone protein HSP33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3314
Polymers26,9931
Non-polymers3383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.420, 96.420, 132.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Probable chaperone protein HSP33 / possible chaperone and cysteine protease HSP33 / Heat shock protein 33


Mass: 26992.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: YOR091C / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08914, Hydrolases; Glycosylases
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: 18% PEG 3000, 200mM (NH4)2SO4, 100mM tri-Sodium Citrate dihytrate, pH 5.6, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→60.63 Å / Num. obs: 45873 / % possible obs: 97.3 % / Redundancy: 2.3 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 8.7 / Num. measured all: 105739
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6819 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QVZ

1qvz


Resolution: 2.4→25.5 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.886 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.223 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 2322 5.1 %RANDOM
Rwork0.22219 43517 --
obs0.22337 43517 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 56.31 Å2 / Biso mean: 21.741 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3635 0 31 168 3834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223747
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9461.9565060
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.3895.085471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84923.951162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89315608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8441516
X-RAY DIFFRACTIONr_chiral_restr0.0690.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212822
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.2571.52318
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.48923714
X-RAY DIFFRACTIONr_scbond_it0.60231429
X-RAY DIFFRACTIONr_scangle_it1.0764.51346
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 157 -
Rwork0.278 3289 -
all-3446 -
obs--99.42 %

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