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- PDB-4gcn: N-terminal domain of stress-induced protein-1 (STI-1) from C.elegans -

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Basic information

Entry
Database: PDB / ID: 4gcn
TitleN-terminal 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 / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. ...STI1/HOP, DP domain / STI1/HOP, DP domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / TPR repeat / Tetratricopeptide 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
TRIETHYLENE GLYCOL / Stress-induced-phosphoprotein 1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 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: N-terminal 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 1.2Feb 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: Protein STI-1
B: Protein STI-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3373
Polymers29,1872
Non-polymers1501
Water3,783210
1
A: Protein STI-1


Theoretical massNumber of molelcules
Total (without water)14,5931
Polymers14,5931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein STI-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7442
Polymers14,5931
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.212, 64.199, 124.933
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein STI-1


Mass: 14593.497 Da / Num. of mol.: 2 / Fragment: N-terminal residues 1-124
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: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M sodium chloride, 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: 1.85→34.9 Å / Num. all: 25569 / Num. obs: 25569 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.079 / Χ2: 1.49 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.85-1.884.50.5852.379551.08674
1.88-1.9250.53910441.11281.7
1.92-1.955.40.45311841.15190
1.95-1.996.40.41712111.1296
1.99-2.047.50.34312851.10899
2.04-2.087.90.26513001.10699.5
2.08-2.148.10.2213001.22499.8
2.14-2.198.10.21112951.20899.2
2.19-2.268.20.17312821.252100
2.26-2.338.10.14713141.28599.8
2.33-2.418.20.14712841.305100
2.41-2.518.20.12213181.28399.8
2.51-2.638.20.11313071.407100
2.63-2.768.30.09213131.444100
2.76-2.948.30.0813341.505100
2.94-3.168.30.06913121.542100
3.16-3.488.30.05813391.647100
3.48-3.998.20.05413482.197100
3.99-5.0280.05313802.436100
5.02-507.50.05614642.51399.4

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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
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→34.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 6.077 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.135 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 1285 5 %RANDOM
Rwork0.1776 ---
all0.1803 25508 --
obs0.1803 25508 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.9 Å2 / Biso mean: 34.241 Å2 / Biso min: 10.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2--4.19 Å20 Å2
3----3.5 Å2
Refinement stepCycle: LAST / Resolution: 1.85→34.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 10 210 2274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022195
X-RAY DIFFRACTIONr_bond_other_d0.0030.021550
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.9522962
X-RAY DIFFRACTIONr_angle_other_deg0.95133798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.565282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9325.254118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82615423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1981511
X-RAY DIFFRACTIONr_chiral_restr0.1050.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022476
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02451
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 59 -
Rwork0.284 1238 -
all-1297 -
obs-1297 72.38 %
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)
11.8493-0.14030.10231.08190.66731.75440.04560.0936-0.0624-0.0249-0.00750.0047-0.01280.0294-0.03810.0133-0.0061-0.00240.012-0.00720.025315.997725.99163.737
23.04240.5809-0.47221.39320.89132.18250.0384-0.03190.11250.0006-0.00860.0074-0.0763-0.0274-0.02980.09040.01340.0070.0038-0.01080.1141-2.198541.583620.3631
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 124
2X-RAY DIFFRACTION2B-2 - 124

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