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- PDB-4fei: Hsp17.7 from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 4fei
TitleHsp17.7 from Deinococcus radiodurans
ComponentsHeat shock protein-related proteinHeat shock response
KeywordsCHAPERONE / stress response / alpha-crystallin domain fold / aggregates / cytosol
Function / homologyImmunoglobulin-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 / Heat shock protein-related protein
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBepperling, A. / Alte, F. / Kriehuber, T. / Braun, N. / Weinkauf, S. / Groll, M. / Haslbeck, M. / Buchner, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Alternative bacterial two-component small heat shock protein systems.
Authors: Bepperling, A. / Alte, F. / Kriehuber, T. / Braun, N. / Weinkauf, S. / Groll, M. / Haslbeck, M. / Buchner, J.
History
DepositionMay 30, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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: Heat shock protein-related protein


Theoretical massNumber of molelcules
Total (without water)10,7361
Polymers10,7361
Non-polymers00
Water1,42379
1
A: Heat shock protein-related protein

A: Heat shock protein-related protein


Theoretical massNumber of molelcules
Total (without water)21,4722
Polymers21,4722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area2670 Å2
ΔGint-8 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.292, 51.292, 80.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-221-

HOH

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Components

#1: Protein Heat shock protein-related protein / Heat shock response


Mass: 10736.011 Da / Num. of mol.: 1 / Fragment: Alpha crystallin domain, UNP RESIDUES 46-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: DR_1691 / Plasmid: 6xHis-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9RTR5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jun 22, 2011
RadiationMonochromator: HELIOS multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 5124 / Num. obs: 5119 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 18.4
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 5.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.5.0109refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3GLA

3gla


Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.895 / SU B: 16.654 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25343 230 4.6 %RANDOM
Rwork0.197 ---
obs0.1996 4778 98.72 %-
all-4778 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.837 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å2-0.49 Å20 Å2
2---0.99 Å20 Å2
3---1.48 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms757 0 0 79 836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022774
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.9851057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.215101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51522.18832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87715113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.292159
X-RAY DIFFRACTIONr_chiral_restr0.1070.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022602
X-RAY DIFFRACTIONr_mcbond_it0.9861.5505
X-RAY DIFFRACTIONr_mcangle_it1.7942808
X-RAY DIFFRACTIONr_scbond_it2.4773269
X-RAY DIFFRACTIONr_scangle_it3.9374.5249
X-RAY DIFFRACTIONr_rigid_bond_restr1.1743774
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 12 -
Rwork0.229 341 -
obs--99.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.52432.79911.79293.71-2.30556.60830.03190.1782-0.4503-0.3674-0.0366-0.39430.67210.3370.00470.26670.01210.0170.209-0.0110.1611-2.7733-7.9065-9.582
20.8504-0.0153-0.00530.1836-0.36270.8699-0.0626-0.01530.05380.01080.08950.0631-0.0532-0.0321-0.02690.180.00570.00190.21970.00790.1639-12.23776.2219-3.8186
31.60054.4325-0.674728.17456.22744.53520.2744-0.23030.17610.8656-0.0921-0.0451-0.00710.2263-0.18230.20210.00860.01330.2894-0.07420.2396-8.45194.38976.8444
44.4702-6.0472-6.605714.781816.30818.0151-0.14330.3339-0.57980.6971-0.47190.57950.8516-0.50320.61520.3486-0.0461-0.03050.1857-0.0140.1851-10.0978-14.4737-12.0853
50.42390.76310.66192.84982.84496.14420.07140.06710.02410.0950.06550.00850.3412-0.138-0.13680.12850.01020.0050.19270.00630.1292-5.0005-8.869-11.7508
61.165-0.2189-1.51342.9142-0.1834.71680.1222-0.09530.07140.0978-0.1232-0.0849-0.2315-0.12730.00090.0922-0.0339-0.01850.207-0.02560.1836-6.562211.35534.6229
71.7291.31660.03631.61220.13460.03530.202-0.1347-0.03580.1233-0.30650.3124-0.0505-0.0880.10440.2520.0652-0.0190.2996-0.06390.2369-17.29866.7046-2.0406
80.7541-1.47050.703917.6575-6.92322.7406-0.05650.177-0.0272-0.1720.0794-0.03440.06060.0004-0.02290.21620.01710.03340.1925-0.03350.1935-13.715423.22380.3617
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 51
2X-RAY DIFFRACTION2A52 - 79
3X-RAY DIFFRACTION3A80 - 90
4X-RAY DIFFRACTION4A91 - 98
5X-RAY DIFFRACTION5A99 - 109
6X-RAY DIFFRACTION6A110 - 119
7X-RAY DIFFRACTION7A120 - 134
8X-RAY DIFFRACTION8A135 - 147

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