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- PDB-4gco: Central domain of stress-induced protein-1 (STI-1) from C.elegans -

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Basic information

Entry
Database: PDB / ID: 4gco
TitleCentral domain of stress-induced protein-1 (STI-1) from C.elegans
ComponentsProtein STI-1
KeywordsPROTEIN BINDING / structural genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / tetratricopeptide repeat domain / TPR domain / Hop / HSP70/HSP90-organising protein / co-chaperone / Hsp70 / Hsp90
Function / homology
Function and homology information


HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / reproductive process / ATPase inhibitor activity / protein folding chaperone complex / protein maturation by protein folding / Hsp70 protein binding / determination of adult lifespan / Hsp90 protein binding / response to heat / cytoplasm
Similarity search - Function
STI1/HOP, DP domain / STI1/HOP, DP domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats ...STI1/HOP, DP domain / STI1/HOP, DP domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / 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
Stress-induced-phosphoprotein 1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsOsipiuk, J. / Bigelow, L. / Gu, M. / Van Oosten-Hawle, P. / Morimoto, R.I. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Central domain of stress-induced protein-1 (STI-1) from C.elegans
Authors: Osipiuk, J. / Bigelow, L. / Gu, M. / Van Oosten-Hawle, P. / Morimoto, R.I. / Joachimiak, A.
History
DepositionJul 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 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

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Assembly

Deposited unit
A: Protein STI-1


Theoretical massNumber of molelcules
Total (without water)14,6101
Polymers14,6101
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.959, 50.570, 72.112
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asymmetric unit

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Components

#1: Protein Protein STI-1


Mass: 14609.541 Da / Num. of mol.: 1 / Fragment: central domain residues 131-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: CELE_R09E12.3, sti-1 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O16259
#2: Water ChemComp-HOH / 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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris buffer, 25% PEG-3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2011
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→29.4 Å / Num. all: 16343 / Num. obs: 16343 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.052 / Χ2: 1.512 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.6-1.633.90.3552.026821.21584
1.63-1.664.60.4937721.26996.3
1.66-1.696.30.3738071.23199.9
1.69-1.728.30.4388231.316100
1.72-1.7690.467961.331100
1.76-1.89.10.3388211.316100
1.8-1.859.10.2658021.286100
1.85-1.99.10.2058061.256100
1.9-1.959.10.1638341.305100
1.95-2.029.20.1177961.336100
2.02-2.099.10.0938301.372100
2.09-2.179.20.0748221.429100
2.17-2.279.10.0668141.419100
2.27-2.399.10.0618301.446100
2.39-2.549.10.0548301.453100
2.54-2.749.10.0478331.451100
2.74-3.018.90.0478401.745100
3.01-3.458.90.0558402.97100
3.45-4.348.60.048552.1699.9
4.34-5080.0329101.48496.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ELW

1elw


Resolution: 1.6→29.4 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 4.38 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.097 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 821 5 %RANDOM
Rwork0.1772 ---
all0.1793 16296 --
obs0.1793 16296 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.87 Å2 / Biso mean: 43.832 Å2 / Biso min: 13.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20 Å2
2---2.5 Å20 Å2
3---1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms978 0 0 147 1125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021077
X-RAY DIFFRACTIONr_bond_other_d0.0010.02783
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.971465
X-RAY DIFFRACTIONr_angle_other_deg0.97531901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2465142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09823.7162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6315209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0051513
X-RAY DIFFRACTIONr_chiral_restr0.1020.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021232
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02233
LS refinement shellResolution: 1.601→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 32 -
Rwork0.331 925 -
all-957 -
obs-957 86.29 %
Refinement TLS params.Method: refined / Origin x: 2.2926 Å / Origin y: -4.3438 Å / Origin z: -7.2988 Å
111213212223313233
T0.1696 Å2-0.0373 Å2-0.0304 Å2-0.0869 Å20.031 Å2--0.0281 Å2
L1.7371 °20.3545 °20.1567 °2-5.8176 °20.1945 °2--0.4505 °2
S0.1125 Å °-0.3669 Å °-0.14 Å °0.9871 Å °-0.1475 Å °-0.1499 Å °0.0281 Å °-0.045 Å °0.035 Å °

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