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- PDB-4j8d: Middle domain of Hsc70-interacting protein, crystal form II -

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Basic information

Entry
Database: PDB / ID: 4j8d
TitleMiddle domain of Hsc70-interacting protein, crystal form II
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 / : / 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 / : / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 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 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: Hsc70-interacting protein
D: Hsc70-interacting protein


Theoretical massNumber of molelcules
Total (without water)79,0454
Polymers79,0454
Non-polymers00
Water00
1
A: Hsc70-interacting protein


Theoretical massNumber of molelcules
Total (without water)19,7611
Polymers19,7611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hsc70-interacting protein


Theoretical massNumber of molelcules
Total (without water)19,7611
Polymers19,7611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Hsc70-interacting protein


Theoretical massNumber of molelcules
Total (without water)19,7611
Polymers19,7611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Hsc70-interacting protein


Theoretical massNumber of molelcules
Total (without water)19,7611
Polymers19,7611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.290, 126.998, 57.312
Angle α, β, γ (deg.)90.00, 105.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

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Components

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


Mass: 19761.188 Da / Num. of mol.: 4 / 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

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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: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.15 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: ID14-4 / Wavelength: 0.9189 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9189 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.594
11L, -K, H20.406
ReflectionResolution: 2.8→63.499 Å / Num. all: 19247 / Num. obs: 19247 / % possible obs: 98.7 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 3.1 % / Rsym value: 0.11 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.8-2.953.10.4271.80.427196
2.95-3.133.20.2812.80.281199.5
3.13-3.343.20.2023.80.202199.3
3.34-3.613.20.1365.60.136199.4
3.61-3.963.10.0918.20.091199.6
3.96-4.423.10.079.90.07199
4.42-5.113.10.06710.40.067199.5
5.11-6.253.10.0917.90.091198.6
6.25-8.853.10.05111.90.051197.8
8.85-43.0363.10.04411.40.044197.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.9 Å43.04 Å
Translation2.9 Å43.04 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4J8F

4j8f


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.864 / Occupancy max: 1 / Occupancy min: 1 / SU B: 20.643 / SU ML: 0.399 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.299 933 4.9 %RANDOM
Rwork0.246 ---
obs0.249 18235 98.4 %-
all-18533 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.26 Å2
Baniso -1Baniso -2Baniso -3
1--34.18 Å20 Å2-5.75 Å2
2--65.9 Å20 Å2
3----31.72 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4884 0 0 0 4884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224952
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0391.9636697
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8635638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.37325.082244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.19915852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5411540
X-RAY DIFFRACTIONr_chiral_restr0.0680.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213810
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2781.53206
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.52825048
X-RAY DIFFRACTIONr_scbond_it0.68831746
X-RAY DIFFRACTIONr_scangle_it1.2374.51649
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1192 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.360.5
2Bmedium positional0.360.5
3Cmedium positional0.40.5
4Dmedium positional0.440.5
1Amedium thermal0.212
2Bmedium thermal0.212
3Cmedium thermal0.222
4Dmedium thermal0.212
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 58 -
Rwork0.311 1226 -
obs--90.49 %

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