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- PDB-1pdw: Crystal structure of human DJ-1, P 1 21 1 space group -

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Basic information

Entry
Database: PDB / ID: 1pdw
TitleCrystal structure of human DJ-1, P 1 21 1 space group
ComponentsDJ-1
KeywordsPROTEIN BINDING / DJ-1
Function / homology
Function and homology information


tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / peptidyl-cysteine deglycation / peptidyl-arginine deglycation / peptidyl-lysine deglycation / protein deglycation, methylglyoxal removal / : / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate ...tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / peptidyl-cysteine deglycation / peptidyl-arginine deglycation / peptidyl-lysine deglycation / protein deglycation, methylglyoxal removal / : / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal removal / cellular detoxification of methylglyoxal / regulation of supramolecular fiber organization / negative regulation of death-inducing signaling complex assembly / negative regulation of TRAIL-activated apoptotic signaling pathway / positive regulation of pyrroline-5-carboxylate reductase activity / positive regulation of tyrosine 3-monooxygenase activity / positive regulation of L-dopa biosynthetic process / positive regulation of L-dopa decarboxylase activity / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / glyoxalase (glycolic acid-forming) activity / negative regulation of protein K48-linked deubiquitination / negative regulation of ubiquitin-specific protease activity / protein deglycation, glyoxal removal / glycolate biosynthetic process / guanine deglycation, glyoxal removal / glyoxal metabolic process / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / detection of oxidative stress / guanine deglycation / positive regulation of NAD(P)H oxidase activity / detoxification of mercury ion / protein deglycase / methylglyoxal metabolic process / positive regulation of mitochondrial electron transport, NADH to ubiquinone / mercury ion binding / hydrogen peroxide metabolic process / protein deglycase activity / positive regulation of dopamine biosynthetic process / oxidoreductase activity, acting on peroxide as acceptor / superoxide dismutase copper chaperone activity / positive regulation of autophagy of mitochondrion / positive regulation of acute inflammatory response to antigenic stimulus / positive regulation of superoxide dismutase activity / lactate biosynthetic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular detoxification of aldehyde / protein deglycosylation / small protein activating enzyme binding / positive regulation of transcription regulatory region DNA binding / Hydrolases; Acting on ester bonds; Thioester hydrolases / peroxiredoxin activity / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of ubiquitin-protein transferase activity / detoxification of copper ion / negative regulation of protein acetylation / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of protein sumoylation / positive regulation of androgen receptor activity / membrane hyperpolarization / negative regulation of protein export from nucleus / regulation of androgen receptor signaling pathway / cupric ion binding / oxygen sensor activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / insulin secretion / ubiquitin-like protein conjugating enzyme binding / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / positive regulation of reactive oxygen species biosynthetic process / nuclear androgen receptor binding / dopamine uptake involved in synaptic transmission / ubiquitin-specific protease binding / cuprous ion binding / cytokine binding / membrane depolarization / single fertilization / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of neuron apoptotic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / activation of protein kinase B activity / adult locomotory behavior / SUMOylation of transcription cofactors / negative regulation of protein phosphorylation / regulation of mitochondrial membrane potential / mitochondrion organization / negative regulation of protein binding / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / adherens junction / kinase binding / negative regulation of protein kinase activity / positive regulation of DNA-binding transcription factor activity / Late endosomal microautophagy / positive regulation of protein-containing complex assembly / PML body / mitochondrial intermembrane space
Similarity search - Function
Protein/nucleic acid deglycase DJ-1 / : / 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
Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTao, X. / Tong, L.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of Human DJ-1, a Protein Associated with Early Onset Parkinson's Disease.
Authors: Tao, X. / Tong, L.
History
DepositionMay 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DJ-1
B: DJ-1
C: DJ-1
D: DJ-1
E: DJ-1
F: DJ-1
G: DJ-1
H: DJ-1


Theoretical massNumber of molelcules
Total (without water)169,4068
Polymers169,4068
Non-polymers00
Water17,475970
1
A: DJ-1
B: DJ-1


Theoretical massNumber of molelcules
Total (without water)42,3522
Polymers42,3522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-19 kcal/mol
Surface area14590 Å2
MethodPISA
2
C: DJ-1
D: DJ-1


Theoretical massNumber of molelcules
Total (without water)42,3522
Polymers42,3522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-19 kcal/mol
Surface area14660 Å2
MethodPISA
3
E: DJ-1
F: DJ-1


Theoretical massNumber of molelcules
Total (without water)42,3522
Polymers42,3522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-19 kcal/mol
Surface area14940 Å2
MethodPISA
4
G: DJ-1
H: DJ-1


Theoretical massNumber of molelcules
Total (without water)42,3522
Polymers42,3522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-18 kcal/mol
Surface area15320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.256, 83.664, 114.159
Angle α, β, γ (deg.)90.00, 100.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DJ-1


Mass: 21175.785 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q99497
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 970 / 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: 1.97 Å3/Da / Density % sol: 37.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG3350, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMTris1reservoirpH8.0
210-12 %(w/v)PEG33501reservoir
315 mg/mlprotein1drop
430 mMTris1droppH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 9, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 69228 / Num. obs: 67190 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 7.1 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.231 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 211982

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.91 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 4695 7.7 %RANDOM
Rwork0.18 ---
obs-61031 91.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.1871 Å2 / ksol: 0.32813 e/Å3
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.24 Å20 Å22.29 Å2
2--0.92 Å20 Å2
3----5.17 Å2
Refine analyzeLuzzati coordinate error free: 0.31 Å / Luzzati sigma a free: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11051 0 0 970 12021
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it2.812.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.275 438 8 %
Rwork0.193 5067 -
obs--83 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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