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- PDB-4j8e: Middle domain of Hsc70-interacting protein, crystal form I -

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Basic information

Entry
Database: PDB / ID: 4j8e
TitleMiddle domain of Hsc70-interacting protein, crystal form I
ComponentsHsc70-interacting protein
KeywordsCHAPERONE / tetratricopeptide repeat / solenoid / Co-chaperone / cytosol
Function / homology
Function and homology information


negative regulation of protein refolding / Regulation of HSF1-mediated heat shock response / dATP binding / histone deacetylase complex / chaperone cofactor-dependent protein refolding / Hsp70 protein binding / response to bacterium / unfolded protein binding / protein-folding chaperone binding / protein dimerization activity ...negative regulation of protein refolding / Regulation of HSF1-mediated heat shock response / dATP binding / histone deacetylase complex / 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
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 domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. ...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 domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Hsc70-interacting protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.6 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 1.2Feb 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,7074
Polymers39,5222
Non-polymers1842
Water19811
1
A: Hsc70-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8532
Polymers19,7611
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hsc70-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8532
Polymers19,7611
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-12 kcal/mol
Surface area12590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.856, 79.856, 97.311
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 19761.188 Da / Num. of mol.: 2 / Fragment: UNP residues 78-247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fam10a1, Hip, St13 / Plasmid: pProEx-HtB / 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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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 Å3/Da / Density % sol: 38.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.3 Na-malonate, pH 6.0, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.00497 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00497 Å / Relative weight: 1
ReflectionRedundancy: 5.1 % / Av σ(I) over netI: 7.7 / Number: 44511 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / D res high: 2.69 Å / D res low: 96.135 Å / Num. obs: 8654 / % possible obs: 97.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
8.5196.1498.210.0310.0314.4
6.028.5199.510.0420.0424.8
4.916.0299.410.0560.0565.3
4.254.9199.610.060.065.2
3.84.2599.310.0680.0685.3
3.473.899.510.0930.0935.6
3.223.4799.910.1730.1735.1
3.013.2299.810.2690.2695.4
2.843.0199.510.3850.3855.4
2.692.8485.610.6090.6094.3
ReflectionResolution: 2.6→96.135 Å / Num. obs: 9666 / % possible obs: 97.5 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 5.1 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 15.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.6-2.844.30.6091.2464710830.60985.6
2.84-3.015.40.3851.9638511770.38599.5
3.01-3.225.40.2692.7605911200.26999.8
3.22-3.475.10.1734.1546810630.17399.9
3.47-3.85.60.0937.753529580.09399.5
3.8-4.255.30.0689.947148870.06899.3
4.25-4.915.20.0610.941438040.0699.6
4.91-6.025.30.05611.836216770.05699.4
6.02-8.514.80.04212.726445480.04299.5
8.51-96.1354.40.0311814783370.03198.2

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Phasing

PhasingMethod: SIRAS
Phasing dmFOM : 0.59 / FOM acentric: 0.59 / FOM centric: 0.6 / Reflection: 10185 / Reflection acentric: 8334 / Reflection centric: 1851
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.4-48.840.940.970.9506289217
4.6-7.40.860.880.8214161056360
3.7-4.60.860.880.7817141387327
3.2-3.70.710.730.6517031426277
2.8-3.20.430.450.3530052576429
2.6-2.80.190.190.1718411600241

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
SHELXphasing
RESOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.2286 / WRfactor Rwork: 0.1734 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.845 / SU B: 20.228 / SU ML: 0.197 / SU R Cruickshank DPI: 0.4591 / SU Rfree: 0.2893 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.459 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 488 4.8 %RANDOM
Rwork0.1841 ---
all0.187 9666 --
obs0.187 9666 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 121.81 Å2 / Biso mean: 50.092 Å2 / Biso min: 20.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 12 11 1888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221905
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9722565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.25236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23225.15895
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.14115345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1271514
X-RAY DIFFRACTIONr_chiral_restr0.0860.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211442
X-RAY DIFFRACTIONr_mcbond_it0.5681.51188
X-RAY DIFFRACTIONr_mcangle_it1.15221880
X-RAY DIFFRACTIONr_scbond_it2.0993717
X-RAY DIFFRACTIONr_scangle_it3.6364.5685
LS refinement shellResolution: 2.6→2.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 43 -
Rwork0.228 667 -
all-710 -
obs--100 %
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)
13.34372.337-0.69035.2634-1.09363.60950.1985-0.26130.00820.263-0.01510.45950.1402-0.2725-0.18340.0871-0.0199-0.02110.1455-0.01670.096165.4508-8.0496-28.2138
28.4056-4.21140.16723.87210.3021.9901-0.02710.0764-0.0762-0.00630.0827-0.32890.21590.0933-0.05560.115-0.03260.00860.0798-0.0290.077896.0884-2.9456-41.3836
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A94 - 212
2X-RAY DIFFRACTION2B95 - 213

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