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- PDB-3uo2: Jac1 co-chaperone from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 3uo2
TitleJac1 co-chaperone from Saccharomyces cerevisiae
ComponentsJ-type co-chaperone JAC1, mitochondrial
KeywordsCHAPERONE / structural genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / co-chaperone / J-protein / iron sulfur cluster biogenesis / Ssq1 Hsp70 chaperone / Isu proteins
Function / homology
Function and homology information


Mitochondrial iron-sulfur cluster biogenesis / protein maturation by [4Fe-4S] cluster transfer / Mitochondrial protein import / protein maturation by [2Fe-2S] cluster transfer / protein maturation by iron-sulfur cluster transfer / [2Fe-2S] cluster assembly / ATPase activator activity / aerobic respiration / mitochondrial intermembrane space / protein complex oligomerization ...Mitochondrial iron-sulfur cluster biogenesis / protein maturation by [4Fe-4S] cluster transfer / Mitochondrial protein import / protein maturation by [2Fe-2S] cluster transfer / protein maturation by iron-sulfur cluster transfer / [2Fe-2S] cluster assembly / ATPase activator activity / aerobic respiration / mitochondrial intermembrane space / protein complex oligomerization / protein-folding chaperone binding / intracellular iron ion homeostasis / mitochondrial inner membrane / mitochondrial matrix / mitochondrion
Similarity search - Function
Co-chaperone Hsc20 / Co-chaperone HscB, C-terminal oligomerisation domain / HSCB C-terminal oligomerisation domain / HscB, C-terminal domain superfamily / HscB, C-terminal domain / DnaJ domain / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Monooxygenase ...Co-chaperone Hsc20 / Co-chaperone HscB, C-terminal oligomerisation domain / HSCB C-terminal oligomerisation domain / HscB, C-terminal domain superfamily / HscB, C-terminal domain / DnaJ domain / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Monooxygenase / Chaperone J-domain superfamily / DnaJ domain / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
J-type co-chaperone JAC1, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsOsipiuk, J. / Mulligan, R. / Bigelow, L. / Marszalek, J. / Craig, E.A. / Dutkiewicz, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Interaction of j-protein co-chaperone jac1 with fe-s scaffold isu is indispensable in vivo and conserved in evolution.
Authors: Ciesielski, S.J. / Schilke, B.A. / Osipiuk, J. / Bigelow, L. / Mulligan, R. / Majewska, J. / Joachimiak, A. / Marszalek, J. / Craig, E.A. / Dutkiewicz, R.
History
DepositionNov 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2May 23, 2012Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: J-type co-chaperone JAC1, mitochondrial
B: J-type co-chaperone JAC1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)41,2352
Polymers41,2352
Non-polymers00
Water1,13563
1
A: J-type co-chaperone JAC1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)20,6171
Polymers20,6171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: J-type co-chaperone JAC1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)20,6171
Polymers20,6171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.606, 60.548, 99.523
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 J-type co-chaperone JAC1, mitochondrial / J-type accessory chaperone 1


Mass: 20617.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: JAC1, SEO2, YGL018C / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P53193
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES buffer, 0.2 M ammonium acetate, 25% PEG-3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / 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: 2.13→29.1 Å / Num. all: 20799 / Num. obs: 20799 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.9 % / Biso Wilson estimate: 53.5 Å2 / Rmerge(I) obs: 0.064 / Χ2: 1.628 / 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
2.13-2.1723.30.8944.710151.298100
2.17-2.2123.20.65210181.328100
2.21-2.2523.30.60810351.298100
2.25-2.2923.20.54710231.365100
2.29-2.3423.30.46510211.339100
2.34-2.423.30.42510071.381100
2.4-2.4623.20.35410301.425100
2.46-2.5323.20.28110381.469100
2.53-2.623.20.24110251.459100
2.6-2.6823.20.19110241.444100
2.68-2.7823.10.15810391.458100
2.78-2.8923.30.13310301.562100
2.89-3.0223.10.10710431.618100
3.02-3.1823.10.08210441.723100
3.18-3.38230.06210341.826100
3.38-3.6422.90.05310532.023100
3.64-4.0122.80.04410662.105100
4.01-4.5922.60.03910512.075100
4.59-5.7822.20.03610871.986100
5.78-5019.70.03611162.41996

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3BVO

3bvo


Resolution: 2.13→29.1 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 12.422 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2733 1065 5.1 %RANDOM
Rwork0.2099 ---
all0.213 20697 --
obs0.213 20697 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.11 Å2 / Biso mean: 57.5866 Å2 / Biso min: 27.37 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å20 Å2
2---2.24 Å20 Å2
3---3.45 Å2
Refinement stepCycle: LAST / Resolution: 2.13→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2585 0 0 63 2648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022729
X-RAY DIFFRACTIONr_bond_other_d0.0010.021926
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.9733696
X-RAY DIFFRACTIONr_angle_other_deg0.98234725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2765330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.31225.208144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.02715542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6991516
X-RAY DIFFRACTIONr_chiral_restr0.1070.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022971
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02529
LS refinement shellResolution: 2.127→2.182 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 62 -
Rwork0.252 1254 -
all-1316 -
obs-1316 95.71 %
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)
13.6463-0.83941.29262.2253-0.29081.9657-0.1027-0.1697-0.22850.17240.04360.0903-0.2036-0.05690.05910.08320.0131-0.02450.02260.00850.034539.808329.4701-0.0152
21.8379-1.78671.8853.9614-2.43222.76360.0251-0.07580.15410.1293-0.1003-0.17510.06710.14490.07520.14630.0415-0.00540.220.03170.04819.463247.822-24.5707
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 178
2X-RAY DIFFRACTION2B11 - 184

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