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- PDB-2f42: dimerization and U-box domains of Zebrafish C-terminal of HSP70 i... -

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Basic information

Entry
Database: PDB / ID: 2f42
Titledimerization and U-box domains of Zebrafish C-terminal of HSP70 interacting protein
ComponentsSTIP1 homology and U-box containing protein 1
KeywordsCHAPERONE / U-box
Function / homology
Function and homology information


cellular response to misfolded protein / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of proteolysis / RING-type E3 ubiquitin transferase / Z disc / protein polyubiquitination / ubiquitin protein ligase activity / protein-folding chaperone binding / proteasome-mediated ubiquitin-dependent protein catabolic process / cytoplasm
Similarity search - Function
Helix Hairpins - #2020 / CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Helix Hairpins ...Helix Hairpins - #2020 / CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Helix Hairpins / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Helix non-globular / Special / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RING-type E3 ubiquitin transferase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsXu, Z. / Nix, J.C. / Misra, S.
CitationJournal: Biochemistry / Year: 2006
Title: Structure and Interactions of the Helical and U-Box Domains of CHIP, the C Terminus of HSP70 Interacting Protein.
Authors: Xu, Z. / Devlin, K.I. / Ford, M.G. / Nix, J.C. / Qin, J. / Misra, S.
History
DepositionNov 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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: STIP1 homology and U-box containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0412
Polymers21,0061
Non-polymers351
Water1,27971
1
A: STIP1 homology and U-box containing protein 1
hetero molecules

A: STIP1 homology and U-box containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0824
Polymers42,0112
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area3050 Å2
ΔGint-53 kcal/mol
Surface area17460 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.499, 100.499, 74.311
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsDimer generated from monomer in asymmetric unit by the operation (-Y, -X, -Z+1/6) and a dx=dy=dz=1 shift

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Components

#1: Protein STIP1 homology and U-box containing protein 1


Mass: 21005.748 Da / Num. of mol.: 1 / Fragment: C-terminal domain, Dimerization domain, U-box
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: stub1 (amino acids 112-284) / Plasmid: PET151-D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q7ZTZ6
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 9% PEG3350, 100mM Bis-Tris, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.2399, 0.9786
DetectorType: NOIR-1 / Detector: CCD / Date: Nov 5, 2005
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.23991
20.97861
ReflectionRedundancy: 20.51 % / Number: 2 / Χ2: 0.96 / D res high: 2.8 Å / D res low: 38.04 Å / Num. obs: 5931 / % possible obs: 100 / Rejects: 412
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRejects
6.0338.0410010.0521.58279
4.796.0310010.0760.8821
4.184.7910010.070.7721
3.84.1810010.0990.8525
3.533.810010.1410.9214
3.323.5310010.2230.9823
3.153.3210010.3120.9716
3.023.1510010.4820.918
2.93.0210010.5590.893
2.82.910010.882
ReflectionResolution: 2.5→50.25 Å / Num. all: 8099 / Num. obs: 8099 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 19.12 % / Biso Wilson estimate: 59.1 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 24.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 18.98 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.7 / % possible all: 100

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.5730.4570.0750.9
2Se600.6310.5420.0630.933
3Se600.8060.2480.0440.705
4Se600.2410.4590.0580.494
Phasing dmFOM : 0.6 / FOM acentric: 0.62 / FOM centric: 0.53 / Reflection: 5770 / Reflection acentric: 4544 / Reflection centric: 1226
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8-19.9240.920.970.87279147132
5-80.850.910.72818572246
4-50.820.860.69983767216
3.5-40.690.730.52979789190
3-3.50.440.470.2817011409292
2.8-30.260.280.191010860150

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Processing

Software
NameVersionClassificationNB
d*TREK9.4LDzdata scaling
SOLVE2.06phasing
RESOLVE2.09phasing
CNS1.1refinement
PDB_EXTRACT1.701data extraction
d*TREKdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.5→50.25 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 424105.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 851 10.6 %RANDOM
Rwork0.266 ---
obs0.266 8008 99 %-
all-8099 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.1699 Å2 / ksol: 0.358994 e/Å3
Displacement parametersBiso mean: 72.7 Å2
Baniso -1Baniso -2Baniso -3
1--16 Å25.32 Å20 Å2
2---16 Å20 Å2
3---32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.5→50.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1144 0 1 71 1216
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.351.5
X-RAY DIFFRACTIONc_mcangle_it3.282
X-RAY DIFFRACTIONc_scbond_it2.512
X-RAY DIFFRACTIONc_scangle_it3.982.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.41 79 10.2 %
Rwork0.41 693 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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