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- PDB-4gaz: Crystal Structure of a Jumonji Domain-containing Protein JMJD5 -

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Basic information

Entry
Database: PDB / ID: 4gaz
TitleCrystal Structure of a Jumonji Domain-containing Protein JMJD5
ComponentsLysine-specific demethylase 8
KeywordsOXIDOREDUCTASE / JmjC domain / demethylase
Function / homology
Function and homology information


[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / wybutosine biosynthetic process / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / methylated histone binding / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression ...[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / wybutosine biosynthetic process / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / methylated histone binding / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization / G2/M transition of mitotic cell cycle / p53 binding / chromosome / fibroblast proliferation / endopeptidase activity / in utero embryonic development / tRNA binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of DNA-templated transcription / proteolysis / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Cupin-like domain 8 / Cupin-like domain / Cupin / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / N-OXALYLGLYCINE / Bifunctional peptidase and arginyl-hydroxylase JMJD5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.81 Å
AuthorsWang, H. / Zhou, X. / Zhang, X. / Tao, Y. / Chen, N. / Zang, J.
CitationJournal: To be Published
Title: Crystal Structure of a Jumonji Domain-containing Protein JMJD5
Authors: Wang, H. / Zhou, X. / Zhang, X. / Tao, Y. / Chen, N. / Zang, J.
History
DepositionJul 26, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysine-specific demethylase 8
B: Lysine-specific demethylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0786
Polymers58,6662
Non-polymers4124
Water30617
1
A: Lysine-specific demethylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5393
Polymers29,3331
Non-polymers2062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine-specific demethylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5393
Polymers29,3331
Non-polymers2062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.431, 69.431, 270.052
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Lysine-specific demethylase 8 / JmjC domain-containing protein 5 / Jumonji domain-containing protein 5


Mass: 29333.229 Da / Num. of mol.: 2 / Fragment: JmjC domain, UNP residues 176-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD5, KDM8 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2
References: UniProt: Q8N371, [histone H3]-dimethyl-L-lysine36 demethylase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 289 K / pH: 7.5
Details: 100mM HEPES, 9% PEG 3350 (w/v), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97922
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.806→40.181 Å / Num. obs: 18410 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 69.32 Å2
Reflection shellResolution: 2.8→2.9 Å / % possible all: 99

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.81→40.18 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.38 / σ(F): 0.18 / Phase error: 29.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2742 907 5.18 %
Rwork0.2213 --
obs0.2239 17495 90.1 %
all-19419 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.555 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso max: 143.34 Å2 / Biso mean: 81.96 Å2 / Biso min: 45.31 Å2
Baniso -1Baniso -2Baniso -3
1-15.5611 Å2-0 Å2-0 Å2
2--15.5611 Å20 Å2
3----31.1223 Å2
Refinement stepCycle: LAST / Resolution: 2.81→40.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3854 0 22 17 3893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093997
X-RAY DIFFRACTIONf_angle_d1.1875442
X-RAY DIFFRACTIONf_dihedral_angle_d18.9591466
X-RAY DIFFRACTIONf_chiral_restr0.08570
X-RAY DIFFRACTIONf_plane_restr0.006706
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8058-2.98160.30341400.27672604274487
2.9816-3.21170.31741600.25022729288991
3.2117-3.53470.3271620.23052810297293
3.5347-4.04580.27621730.20922889306296
4.0458-5.09570.22521410.18292722286388
5.0957-40.18480.25451310.22772834296586

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