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- PDB-3uo3: Jac1 co-chaperone from Saccharomyces cerevisiae, 5-182 clone -

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Basic information

Entry
Database: PDB / ID: 3uo3
TitleJac1 co-chaperone from Saccharomyces cerevisiae, 5-182 clone
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
ACETATE ION / J-type co-chaperone JAC1, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsOsipiuk, J. / Bigelow, L. / Mulligan, R. / Feldmann, B. / Babnigg, G. / 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 1.3May 22, 2013Group: Structure summary
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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: J-type co-chaperone JAC1, mitochondrial
B: J-type co-chaperone JAC1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6433
Polymers42,5842
Non-polymers591
Water2,936163
1
A: J-type co-chaperone JAC1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3512
Polymers21,2921
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: J-type co-chaperone JAC1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)21,2921
Polymers21,2921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.791, 60.450, 108.886
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: 21292.107 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: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53193
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.085 M Tris-HCl buffer, 0.17 M sodium acetate, 25.5% PEG-4000, pH 8.5, 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→40.5 Å / Num. all: 34454 / Num. obs: 34454 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.071 / Χ2: 1.694 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.85-1.886.10.7912.2116831.09699.7
1.88-1.928.50.78616941.15399.9
1.92-1.9511.40.75416771.15699.9
1.95-1.9912.30.60717041.1999.9
1.99-2.0413.50.49717061.183100
2.04-2.08140.43716921.249100
2.08-2.1414.50.34917061.267100
2.14-2.1914.80.28617011.282100
2.19-2.2614.80.23316881.43100
2.26-2.3314.80.20117261.39100
2.33-2.4114.80.17217071.413100
2.41-2.5114.80.14117161.513100
2.51-2.6314.80.11817111.604100
2.63-2.7614.90.10117241.685100
2.76-2.9414.90.08717291.815100
2.94-3.1614.80.07317342.171100
3.16-3.4814.50.06317272.659100
3.48-3.9914.10.05717632.96599.9
3.99-5.0213.70.04717952.472100
5.02-50130.04218712.32499.2

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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 3UO2

3uo2


Resolution: 1.85→40.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.419 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 1736 5 %RANDOM
Rwork0.1921 ---
all0.1943 34392 --
obs0.1943 34392 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 140.65 Å2 / Biso mean: 56.9596 Å2 / Biso min: 20.17 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å20 Å2
2---1.96 Å20 Å2
3---3.13 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2676 0 4 163 2843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022808
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.9713807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5465342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87925.17147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.64115551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.211517
X-RAY DIFFRACTIONr_chiral_restr0.1290.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212120
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 122 -
Rwork0.319 2147 -
all-2269 -
obs-2269 98.4 %
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)
11.52110.4180.20371.5961-0.04570.0343-0.11630.10890.0524-0.03790.11230.0778-0.01530.00990.00390.0097-0.0065-0.010.027-0.00320.073313.51574.040526.4485
22.65793.0081-1.74395.1-2.32123.3790.14590.1950.2581-0.26690.15790.1415-0.4945-0.0728-0.30380.5577-0.0281-0.00510.48280.01850.299130.082827.04021.0203
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 181
2X-RAY DIFFRACTION2B12 - 176

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