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- PDB-1gme: Crystal structure and assembly of an eukaryotic small heat shock ... -

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Basic information

Entry
Database: PDB / ID: 1gme
TitleCrystal structure and assembly of an eukaryotic small heat shock protein
ComponentsHEAT SHOCK PROTEIN 16.9B
KeywordsCHAPERONE / SMALL HEAT SHOCK PROTEIN / ALPHA-CRYSTALLIN
Function / homology
Function and homology information


protein complex oligomerization / response to salt stress / response to hydrogen peroxide / protein homooligomerization / unfolded protein binding / protein folding / response to heat / cytoplasm
Similarity search - Function
: / 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
16.9 kDa class I heat shock protein 2
Similarity search - Component
Biological speciesTRITICUM AESTIVUM (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsVan Montfort, R.L.M. / Basha, E. / Friedrich, K.L. / Slingsby, C. / Vierling, E.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Crystal Structure and Assembly of an Eukaryotic Small Heat Shock Protein
Authors: Van Montfort, R.L.M. / Basha, E. / Friedrich, K.L. / Slingsby, C. / Vierling, E.
History
DepositionSep 13, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEAT SHOCK PROTEIN 16.9B
B: HEAT SHOCK PROTEIN 16.9B
C: HEAT SHOCK PROTEIN 16.9B
D: HEAT SHOCK PROTEIN 16.9B


Theoretical massNumber of molelcules
Total (without water)67,5254
Polymers67,5254
Non-polymers00
Water59433
1
A: HEAT SHOCK PROTEIN 16.9B
B: HEAT SHOCK PROTEIN 16.9B
x 6


Theoretical massNumber of molelcules
Total (without water)202,57412
Polymers202,57412
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
MethodPQS
2
C: HEAT SHOCK PROTEIN 16.9B
D: HEAT SHOCK PROTEIN 16.9B
x 6


Theoretical massNumber of molelcules
Total (without water)202,57412
Polymers202,57412
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation6_557-x,-x+y,-z+21
crystal symmetry operation5_557x-y,-y,-z+21
crystal symmetry operation4_557y,x,-z+21
MethodPQS
Unit cell
Length a, b, c (Å)171.645, 171.645, 124.157
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.78, 0.4595, 0.4248), (0.4615, -0.0361, 0.8864), (0.4226, 0.8875, -0.1839)-19.0542, -48.3981, 62.4818
2given(0.5066, 0.8622, -0.0016), (0.8622, -0.5066, -0.0008), (-0.0015, -0.0009, -1)0.157, 0.0572, 186.455
3given(-0.0293, -0.8871, -0.4606), (0.22, 0.4438, -0.8687), (0.9751, -0.1268, 0.1822)65.2462, 114.1278, 28.1291

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Components

#1: Protein
HEAT SHOCK PROTEIN 16.9B


Mass: 16881.168 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRITICUM AESTIVUM (bread wheat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q41560
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE SHOWS SER AT POSITION 7 INSTEAD OF THR AS REPORTED IN THE SWISSPROT ENTRY. SUBSEQUENT ...THE SEQUENCE SHOWS SER AT POSITION 7 INSTEAD OF THR AS REPORTED IN THE SWISSPROT ENTRY. SUBSEQUENT RESEQUENCING HAS CONFIRMED A SERINE RESIDUE AT POSITION 7

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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: 2.59 Å3/Da / Density % sol: 52 % / Description: MAD DATA COLLECTED ON BM14
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 26-29% PEG400, 0.2M SODIUM CITRATE, 0.1M TRIS/HCL PH8.5, pH 8.50
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
126-29 %(v/v)PEG4001reservoir
20.2 Msodium citrate1reservoir
30.1 MTris-HCl1reservoirpH8.5
41 mMEDTA1drop
52 mMdithiothreitol1drop
610 mMTris-HCl1droppH7.0
78 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. obs: 19276 / % possible obs: 94.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 4 / % possible all: 96.7
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. measured all: 170065 / Rmerge(I) obs: 0.04

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
SnBV. 2.1phasing
SHARPphasing
SOLOMONphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→30 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.286 886 4.6 %RANDOM
Rwork0.231 ---
obs0.231 19276 93.8 %-
Displacement parametersBiso mean: 33.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.496 Å2-6.677 Å20 Å2
2---3.496 Å20 Å2
3---6.993 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4107 0 0 33 4140
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.7092
X-RAY DIFFRACTIONc_scbond_it1.5582
X-RAY DIFFRACTIONc_scangle_it2.5992
LS refinement shellResolution: 2.7→2.76 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.424 49 4.7 %
Rwork0.353 1052 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4

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