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- PDB-4ofw: Crystal Structure of Arabidopsis thaliana DJ-1d -

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Basic information

Entry
Database: PDB / ID: 4ofw
TitleCrystal Structure of Arabidopsis thaliana DJ-1d
ComponentsProtein DJ-1 homolog D
KeywordsLYASE / Glyoxalase
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChoi, D. / Kim, J. / Ryu, K.-S. / Park, C.
CitationJournal: Febs J. / Year: 2014
Title: Stereospecific mechanism of DJ-1 glyoxalases inferred from their hemithioacetal-containing crystal structures.
Authors: Choi, D. / Kim, J. / Ha, S. / Kwon, K. / Kim, E.H. / Lee, H.Y. / Ryu, K.S. / Park, C.
History
DepositionJan 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type
Revision 1.4Sep 20, 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: Protein DJ-1 homolog D
B: Protein DJ-1 homolog D
C: Protein DJ-1 homolog D
D: Protein DJ-1 homolog D
E: Protein DJ-1 homolog D
F: Protein DJ-1 homolog D


Theoretical massNumber of molelcules
Total (without water)249,8126
Polymers249,8126
Non-polymers00
Water9,764542
1
A: Protein DJ-1 homolog D
B: Protein DJ-1 homolog D
C: Protein DJ-1 homolog D


Theoretical massNumber of molelcules
Total (without water)124,9063
Polymers124,9063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-18 kcal/mol
Surface area38070 Å2
MethodPISA
2
D: Protein DJ-1 homolog D
E: Protein DJ-1 homolog D
F: Protein DJ-1 homolog D


Theoretical massNumber of molelcules
Total (without water)124,9063
Polymers124,9063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-12 kcal/mol
Surface area38210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.556, 115.047, 115.531
Angle α, β, γ (deg.)90.000, 91.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein DJ-1 homolog D / AtDJ1D / Lactoylglutathione lyase DJ1D


Mass: 41635.344 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DJ1D, At3g02720, F13E7.34 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9M8R4, D-lactate dehydratase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium citrate, 15% 2-propanol, 16% PEG4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 31, 2011
RadiationMonochromator: cryocooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 117444 / % possible obs: 95.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.11 / Χ2: 3.536 / Net I/av σ(I): 15.338 / Net I/σ(I): 14.6
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.382.70.345109341.24290.1
2.38-2.482.80.325111281.25691
2.48-2.593.20.279114031.39593.6
2.59-2.733.50.257115711.99595
2.73-2.93.90.199117881.78496.3
2.9-3.124.50.169119522.14397.5
3.12-3.445.30.134119972.85198.3
3.44-3.9360.102121284.28198.9
3.93-4.956.40.079121845.46998.9
4.95-506.40.071123596.06499.2

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Processing

Software
NameVersionClassificationNB
CNSrefinement
REFMACrefinement
PDB_EXTRACT3.14data extraction
HKL-2000data reduction
Cootmodel building
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PDV

1pdv


Resolution: 2.3→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.284 11742 9.6 %
Rwork0.2428 --
obs-117422 95.9 %
Displacement parametersBiso max: 74.62 Å2 / Biso mean: 32.1717 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--9.915 Å20 Å2-2.573 Å2
2---5.585 Å20 Å2
3---15.5 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17544 0 0 542 18086
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.318
X-RAY DIFFRACTIONc_mcbond_it1.2241.5
X-RAY DIFFRACTIONc_scbond_it1.8642
X-RAY DIFFRACTIONc_mcangle_it2.0332
X-RAY DIFFRACTIONc_scangle_it2.7752.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.380.433211010.419397811088289.6
2.38-2.480.414811590.398599741113391
2.48-2.590.387211100.3516103061141693.6
2.59-2.730.350110890.313104861157595
2.73-2.90.318911630.2828106221178596.3
2.9-3.120.312112010.2634107601196197.5
3.12-3.440.295412240.2375107771200198.3
3.44-3.930.251612350.1975108961213199
3.93-4.950.202512370.1541109481218598.9
4.95-500.200912230.164111301235399.3
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna -rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6edo_cns.param

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