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- PDB-3uk7: Crystal Structure of Arabidopsis thaliana DJ-1D -

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Basic information

Entry
Database: PDB / ID: 3uk7
TitleCrystal Structure of Arabidopsis thaliana DJ-1D
ComponentsClass I glutamine amidotransferase-like domain-containing protein
KeywordsTRANSFERASE / Rossmann Fold / cytosol
Function / homology
Function and homology information


glyoxalase III activity / lactoylglutathione lyase / lactoylglutathione lyase activity / cytosol
Similarity search - Function
Deglycase PfpI / PfpI endopeptidase domain profile. / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein DJ-1 homolog D
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsSeo, K.H. / Zhuang, N.N. / Son, D.Y. / Lee, K.H.
CitationJournal: To be Published
Title: Crystal Structure of Arabidopsis DJ-1D
Authors: Seo, K.H. / Zhuang, N.N. / Son, D.Y. / Lee, K.H.
History
DepositionNov 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Class I glutamine amidotransferase-like domain-containing protein
B: Class I glutamine amidotransferase-like domain-containing protein
C: Class I glutamine amidotransferase-like domain-containing protein


Theoretical massNumber of molelcules
Total (without water)128,4533
Polymers128,4533
Non-polymers00
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-20 kcal/mol
Surface area38630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.778, 75.214, 141.673
Angle α, β, γ (deg.)90.00, 96.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A3 - 338
2114B3 - 338
3114C3 - 338

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Components

#1: Protein Class I glutamine amidotransferase-like domain-containing protein / DJ-1d / F13E7.34 protein / Putative uncharacterized protein At3g02720


Mass: 42817.691 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DJ-1D / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9M8R4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE (-4) RESIDUE IS MET. THE AUTHOR COULD NOT FOUND THE HEAVY ATOM AT -4 RESIDUE POSITION.

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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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.22M NaCl, 0.1M Bis-Tri, 21% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 0.97954, 0.97955, 0.98736
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 27, 2008
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979541
20.979551
30.987361
ReflectionResolution: 2.05→45.1 Å / Num. all: 73962 / Num. obs: 70208 / % possible obs: 97.48 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 2.05 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.05→45.1 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.112 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0.5 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22477 3722 5 %RANDOM
Rwork0.17394 ---
obs0.17657 70208 99.51 %-
all-73962 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.063 Å2
Baniso -1Baniso -2Baniso -3
1-2.41 Å20 Å2-0.02 Å2
2---1.05 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.05→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8816 0 0 336 9152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0229023
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9531.96412283
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26551165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53724.661369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.721151397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4511531
X-RAY DIFFRACTIONr_chiral_restr0.1410.21393
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216881
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_it0.9611.55795
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58629322
X-RAY DIFFRACTIONr_scbond_it3.00833228
X-RAY DIFFRACTIONr_scangle_it4.3114.52961
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2540 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.290.5
Bmedium positional0.30.5
Cmedium positional0.30.5
Amedium thermal1.172
Bmedium thermal1.232
Cmedium thermal1.182
LS refinement shellResolution: 2.052→2.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 264 -
Rwork0.243 5081 -
obs--97.36 %
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)
10.3378-0.2171-0.04410.76350.08180.8911-0.0083-0.001-0.00270.1504-0.0173-0.05480.10620.07310.02560.0506-0.007-0.02060.02660.01340.032844.245231.779853.7041
20.3528-0.11640.06370.960.1210.92750.00920.03190.0554-0.0777-0.03950.009-0.1364-0.10140.03030.0260.01650.00570.0310.00480.058229.159967.311937.9551
30.4017-0.3268-0.16081.15630.05831.20820.05650.05680.0383-0.1735-0.0377-0.1096-0.02540.0784-0.01880.02690.00160.01410.06490.00690.03544.358137.587812.1948
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 388
2X-RAY DIFFRACTION2B3 - 388
3X-RAY DIFFRACTION3C-7 - 388

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