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- PDB-4gjz: JMJD5 in complex with 2-oxoglutarate -

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Basic information

Entry
Database: PDB / ID: 4gjz
TitleJMJD5 in complex with 2-oxoglutarate
ComponentsJmjC domain-containing protein 5
KeywordsOXIDOREDUCTASE / JmjC / beta barrel / Fe(II) and 2-oxoglutarate binding
Function / homology
Function and homology information


[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / 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 ...[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / 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 / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of DNA-templated transcription / proteolysis / nucleoplasm / metal ion binding / nucleus / 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
2-OXOGLUTARIC ACID / BETA-MERCAPTOETHANOL / : / Bifunctional peptidase and arginyl-hydroxylase JMJD5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.0481 Å
AuthorsDel Rizzo, P.A. / Trievel, R.C.
CitationJournal: Mol.Cell.Biol. / Year: 2012
Title: Crystal Structure and Functional Analysis of JMJD5 Indicate an Alternate Specificity and Function.
Authors: Del Rizzo, P.A. / Krishnan, S. / Trievel, R.C.
History
DepositionAug 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Nov 14, 2012Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: JmjC domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5454
Polymers27,2621
Non-polymers2833
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.695, 64.056, 76.801
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 JmjC domain-containing protein 5 / JmjC domain-containing protein 5 / Jumonji domain-containing protein 5


Mass: 27261.873 Da / Num. of mol.: 1 / Fragment: JmjC Domain (UNP Residues 183-416)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD5, JMJD5 (Amino Acids 183 - 416), KDM8 / Plasmid: pDR146 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(Rosetta2)
References: UniProt: Q8N371, [histone H3]-dimethyl-L-lysine36 demethylase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 9.5% PEG 3000, 0.1 M Bis-Tris pH 6.2, 0.05 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 8, 2010
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.048→100 Å / Num. obs: 110949 / % possible obs: 96.5 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.089 / Χ2: 1.005 / Net I/σ(I): 16.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.048-1.093.60.45386441.13176.2
1.09-1.138.50.391112691.204199
1.13-1.1812.70.334113751.2291100
1.18-1.2413.80.258113831.1861100
1.24-1.3214.10.209114301.1361100
1.32-1.4314.30.157114541.0091100
1.43-1.5714.40.114114340.9141100
1.57-1.814.60.096115340.9491100
1.8-2.2614.70.074116010.8641100
2.26-100130.071108250.616190.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å25.41 Å
Translation2.5 Å25.41 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.0481→25.406 Å / Occupancy max: 1 / Occupancy min: 0.16 / SU ML: 0.29 / σ(F): 0.07 / Phase error: 11.8 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1628 1846 1.72 %
Rwork0.1472 --
obs0.1475 107255 92.95 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.254 Å2 / ksol: 0.387 e/Å3
Displacement parametersBiso max: 48.25 Å2 / Biso mean: 15.0812 Å2 / Biso min: 4.47 Å2
Baniso -1Baniso -2Baniso -3
1-2.8041 Å2-0 Å2-0 Å2
2---2.7406 Å20 Å2
3----0.0634 Å2
Refinement stepCycle: LAST / Resolution: 1.0481→25.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1846 0 15 486 2347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082155
X-RAY DIFFRACTIONf_angle_d1.3122982
X-RAY DIFFRACTIONf_chiral_restr0.082315
X-RAY DIFFRACTIONf_plane_restr0.008396
X-RAY DIFFRACTIONf_dihedral_angle_d15.246840
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0481-1.07650.3185850.30684854493956
1.0765-1.10820.24911240.2417398752286
1.1082-1.14390.18191420.16558089823194
1.1439-1.18480.13261380.12448306844496
1.1848-1.23220.12791460.11258350849697
1.2322-1.28830.13371530.1198422857597
1.2883-1.35620.13391500.12148524867498
1.3562-1.44120.13021520.12498553870599
1.4412-1.55250.14121540.12568659881399
1.5525-1.70870.14821520.125986788830100
1.7087-1.95580.15341550.134987438898100
1.9558-2.46380.15841570.139688368993100
2.4638-25.41310.18991380.1767997813588

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