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- PDB-1fpo: HSC20 (HSCB), A J-TYPE CO-CHAPERONE FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1fpo
TitleHSC20 (HSCB), A J-TYPE CO-CHAPERONE FROM E. COLI
ComponentsCHAPERONE PROTEIN HSCB
KeywordsCHAPERONE / molecular chaperone
Function / homology
Function and homology information


iron-sulfur cluster transfer complex / protein maturation by iron-sulfur cluster transfer / [2Fe-2S] cluster assembly / ATPase activator activity / protein folding / protein complex oligomerization / protein-folding chaperone binding / cytosol / cytoplasm
Similarity search - Function
Co-chaperone Hsc20 / Co-chaperone HscB, C-terminal oligomerisation domain / HSCB C-terminal oligomerisation domain / HscB, C-terminal domain superfamily / HscB, C-terminal domain / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Monooxygenase / Chaperone J-domain superfamily ...Co-chaperone Hsc20 / Co-chaperone HscB, C-terminal oligomerisation domain / HSCB C-terminal oligomerisation domain / HscB, C-terminal domain superfamily / HscB, C-terminal domain / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Monooxygenase / Chaperone J-domain superfamily / DnaJ domain / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Co-chaperone protein HscB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsCupp-Vickery, J.R. / Vickery, L.E.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of Hsc20, a J-type Co-chaperone from Escherichia coli.
Authors: Cupp-Vickery, J.R. / Vickery, L.E.
History
DepositionAug 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHAPERONE PROTEIN HSCB
B: CHAPERONE PROTEIN HSCB
C: CHAPERONE PROTEIN HSCB


Theoretical massNumber of molelcules
Total (without water)60,5033
Polymers60,5033
Non-polymers00
Water8,089449
1
A: CHAPERONE PROTEIN HSCB


Theoretical massNumber of molelcules
Total (without water)20,1681
Polymers20,1681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CHAPERONE PROTEIN HSCB


Theoretical massNumber of molelcules
Total (without water)20,1681
Polymers20,1681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CHAPERONE PROTEIN HSCB


Theoretical massNumber of molelcules
Total (without water)20,1681
Polymers20,1681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: CHAPERONE PROTEIN HSCB

A: CHAPERONE PROTEIN HSCB
C: CHAPERONE PROTEIN HSCB


Theoretical massNumber of molelcules
Total (without water)60,5033
Polymers60,5033
Non-polymers00
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation2_555-x,y,-z1
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-14 kcal/mol
Surface area26400 Å2
MethodPISA
5
A: CHAPERONE PROTEIN HSCB

C: CHAPERONE PROTEIN HSCB

B: CHAPERONE PROTEIN HSCB


Theoretical massNumber of molelcules
Total (without water)60,5033
Polymers60,5033
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_554-x,y,-z-11
Buried area3330 Å2
ΔGint-19 kcal/mol
Surface area27390 Å2
MethodPISA
6
A: CHAPERONE PROTEIN HSCB

B: CHAPERONE PROTEIN HSCB


Theoretical massNumber of molelcules
Total (without water)40,3352
Polymers40,3352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area1740 Å2
ΔGint-9 kcal/mol
Surface area19720 Å2
MethodPISA
7
B: CHAPERONE PROTEIN HSCB

C: CHAPERONE PROTEIN HSCB


Theoretical massNumber of molelcules
Total (without water)40,3352
Polymers40,3352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1590 Å2
ΔGint-9 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.010, 69.990, 68.110
Angle α, β, γ (deg.)90.00, 98.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-245-

HOH

21C-220-

HOH

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Components

#1: Protein CHAPERONE PROTEIN HSCB / / HSC20


Mass: 20167.695 Da / Num. of mol.: 3 / Mutation: V148C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6L9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400 Hepes Magnesium Chloride Dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %(w/v)PEG4001reservoir
20.1 MHEPES1reservoir
30.1 M1reservoirMgCl2
41-10 %(w/v)dioxane1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21031
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL7-111
SYNCHROTRONSSRL BL1-521.4
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEMar 1, 1999
OTHER2CCDMar 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.41
ReflectionResolution: 1.8→50 Å / Num. all: 53136 / Num. obs: 52919 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 12.7
Reflection shellResolution: 1.8→1.9 Å / Num. unique all: 7811 / % possible all: 98.7
Reflection
*PLUS
Num. obs: 53718 / % possible obs: 98.7 % / Num. measured all: 171482
Reflection shell
*PLUS
% possible obs: 97.7 % / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementResolution: 1.8→48.73 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1717346.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 5388 10.2 %RANDOM
Rwork0.216 ---
obs0.216 52919 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.85 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20 Å22.63 Å2
2--1.89 Å20 Å2
3----3.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4082 0 0 449 4531
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d16.7
X-RAY DIFFRACTIONc_improper_angle_d0.62
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 912 10.5 %
Rwork0.288 7811 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / Num. reflection obs: 47531
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.912
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.62

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