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- PDB-3ag7: An auxilin-like J-domain containing protein, JAC1 J-domain -

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Basic information

Entry
Database: PDB / ID: 3ag7
TitleAn auxilin-like J-domain containing protein, JAC1 J-domain
ComponentsPutative uncharacterized protein F9E10.5
KeywordsPLANT PROTEIN / J-domain / An auxilin-like J-domain containing protein / JAC1 / CHLOROPLAST ACCUMULATION RESPONSE
Function / homology
Function and homology information


response to photooxidative stress / chloroplast avoidance movement / chloroplast accumulation movement / cellular response to blue light / actin filament organization / mitochondrion / cytoplasm
Similarity search - Function
DnaJ domain / Chaperone J-domain superfamily / DnaJ domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
J domain-containing protein required for chloroplast accumulation response 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTakano, A.
CitationJournal: Plant Cell.Physiol. / Year: 2010
Title: Crystallographic and functional analyses of J-domain of JAC1 essential for chloroplast photorelocation movement in Arabidopsis thaliana
Authors: Takano, A. / Suetsugu, N. / Wada, M. / Kohda, D.
History
DepositionMar 24, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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: Putative uncharacterized protein F9E10.5


Theoretical massNumber of molelcules
Total (without water)11,9411
Polymers11,9411
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.432, 39.477, 68.954
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein F9E10.5 / At1g75100/F9E10_5 / Auxilin-like J-domain protein


Mass: 11940.745 Da / Num. of mol.: 1 / Fragment: J-domain, UNP residues 551-651
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Columbia / Gene: At1g75100, F9E10.5, JAC1 / Plasmid: pGEX-6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9C9Q4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.85 Å3/Da / Density % sol: 33.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES, 30% (v/v) Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 8688 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.043 / Net I/σ(I): 38.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 11.3 / Num. unique all: 855 / Rsym value: 0.155 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QWN

2qwn


Resolution: 1.8→9.98 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.91 / SU B: 2.703 / SU ML: 0.088 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 405 4.7 %RANDOM
Rwork0.17194 ---
obs0.17483 8180 99.86 %-
all-8688 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.121 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→9.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms833 0 0 104 937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022858
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9611158
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6265106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10324.86537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98915161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.284154
X-RAY DIFFRACTIONr_chiral_restr0.0990.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021638
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2671.5523
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2032836
X-RAY DIFFRACTIONr_scbond_it3.9423335
X-RAY DIFFRACTIONr_scangle_it6.4924.5321
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 30 -
Rwork0.169 565 -
obs-565 99.33 %

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