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- PDB-4j8c: Crystal structure of the dimerization domain of Hsc70-interacting... -

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Basic information

Entry
Database: PDB / ID: 4j8c
TitleCrystal structure of the dimerization domain of Hsc70-interacting protein
ComponentsHsc70-interacting protein
KeywordsCHAPERONE / alpha helical dimer / Co-chaperone / cytosol
Function / homology
Function and homology information


negative regulation of protein refolding / Regulation of HSF1-mediated heat shock response / dATP binding / chaperone cofactor-dependent protein refolding / Hsp70 protein binding / response to bacterium / unfolded protein binding / protein-folding chaperone binding / protein dimerization activity / protein domain specific binding ...negative regulation of protein refolding / Regulation of HSF1-mediated heat shock response / dATP binding / chaperone cofactor-dependent protein refolding / Hsp70 protein binding / response to bacterium / unfolded protein binding / protein-folding chaperone binding / protein dimerization activity / protein domain specific binding / protein-containing complex binding / protein-containing complex / identical protein binding / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3420 / Hsp70-interacting protein, N-terminal / Hsp70-interacting protein N N-terminal domain / STI1/HOP, DP domain / STI1/HOP, DP domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Tetratricopeptide repeat / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / TPR repeat region circular profile. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3420 / Hsp70-interacting protein, N-terminal / Hsp70-interacting protein N N-terminal domain / STI1/HOP, DP domain / STI1/HOP, DP domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Tetratricopeptide repeat / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Helix non-globular / Special / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Hsc70-interacting protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.1 Å
AuthorsLi, Z. / Bracher, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structure and function of Hip, an attenuator of the Hsp70 chaperone cycle.
Authors: Li, Z. / Hartl, F.U. / Bracher, A.
History
DepositionFeb 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Jun 6, 2018Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hsc70-interacting protein
B: Hsc70-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7753
Polymers10,6832
Non-polymers921
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-25 kcal/mol
Surface area5450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.775, 43.978, 32.211
Angle α, β, γ (deg.)90.000, 93.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Hsc70-interacting protein / Hip / Protein FAM10A1 / Protein ST13 homolog


Mass: 5341.260 Da / Num. of mol.: 2 / Fragment: UNP residues 1-44
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fam10a1, Hip, St13 / Plasmid: pETM30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) cod+ RIL / References: UniProt: P50503
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 1.9 Å3/Da / Density % sol: 35.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.52 Na-malonate, pH 7.0, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.90004 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90004 Å / Relative weight: 1
ReflectionRedundancy: 7.3 % / Av σ(I) over netI: 4.6 / Number: 94893 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / D res high: 1.493 Å / D res low: 43.895 Å / Num. obs: 12978 / % possible obs: 98.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
4.7243.999.710.0540.0547.1
3.344.7210010.050.057.4
2.733.3410010.0720.0727.2
2.362.7310010.0880.0887.3
2.112.3610010.110.117.4
1.932.1110010.1530.1537.4
1.781.9399.910.2270.2277.4
1.671.7899.810.2970.2977.3
1.571.6799.710.3750.3757.3
1.491.5792.410.5130.5137.2
ReflectionResolution: 1.1→43.98 Å / Num. all: 32315 / Num. obs: 32315 / % possible obs: 98.6 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 3.6 % / Biso Wilson estimate: 7.173 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 13.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.1-1.163.50.32321623646400.32397.5
1.16-1.233.60.2352.71607644890.23599.8
1.23-1.313.60.173.71532342620.17100
1.31-1.423.60.1324.81425839460.132100
1.42-1.553.60.0876.91320336310.087100
1.55-1.743.60.0688.81200933060.068100
1.74-23.60.05410.91049929160.054100
2-2.463.70.03715.6921624620.037100
2.46-3.473.60.03515.2686318910.03598.2
3.47-43.983.10.0378.824027720.03771.2

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
SHELXphasing
SHELXmodel building
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.1→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1552 / WRfactor Rwork: 0.1298 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9235 / SU B: 0.871 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0321 / SU Rfree: 0.0325 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1618 1598 5 %RANDOM
Rwork0.1349 ---
all0.1363 31136 --
obs0.1363 30476 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.78 Å2 / Biso mean: 14.8781 Å2 / Biso min: 4.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.04 Å2
2--0.01 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms720 0 6 147 873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022852
X-RAY DIFFRACTIONr_bond_other_d0.0020.02650
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.9871155
X-RAY DIFFRACTIONr_angle_other_deg0.96931575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8655109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.35821.79539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44515170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.0671512
X-RAY DIFFRACTIONr_chiral_restr0.0940.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02975
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02183
X-RAY DIFFRACTIONr_nbd_refined0.2660.2249
X-RAY DIFFRACTIONr_nbd_other0.2190.2789
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2451
X-RAY DIFFRACTIONr_nbtor_other0.0880.2443
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2102
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.320.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.222
X-RAY DIFFRACTIONr_mcbond_it2.7571.5678
X-RAY DIFFRACTIONr_mcbond_other0.8381.5195
X-RAY DIFFRACTIONr_mcangle_it3.1342850
X-RAY DIFFRACTIONr_scbond_it4.6733379
X-RAY DIFFRACTIONr_scangle_it6.2474.5304
X-RAY DIFFRACTIONr_rigid_bond_restr1.99531833
X-RAY DIFFRACTIONr_sphericity_free7.7023147
X-RAY DIFFRACTIONr_sphericity_bonded5.97231475
LS refinement shellResolution: 1.1→1.127 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.166 117 -
Rwork0.18 2128 -
all-2245 -
obs--93.66 %

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