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- PDB-7yxj: Drosophila melanogaster JMJD7 (dmJMJD7) in complex with Mn and 2,... -

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Basic information

Entry
Database: PDB / ID: 7yxj
TitleDrosophila melanogaster JMJD7 (dmJMJD7) in complex with Mn and 2,4-PDCA
ComponentsGH14974p
KeywordsOXIDOREDUCTASE / NON-HEME / IRON / 2-OXOGLUTARATE / DIOXYGENASE / OXYGENASE / JMJC / JMJC DOMAIN / JMJC DOMAIN-CONTAINING PROTEIN 7 / JMJD7 / JMJC HYDROXYLASE / JMJC DEMETHYLASE / KDMS / POST-TRANSLATIONAL MODIFICATIONS / PTM / HYDROXYLATION / LYSYL HYDROXYLATION / DIMERISATION / TRANSLATION FACTOR / DEVELOPMENTALLY REGULATED GTP BINDING PROTEINS / DRG1 / DRG2 / TRAFAC GTPASE / HYPOXIA / NUCLEIC ACID- BINDING / METAL-BINDING / TRANSLATION / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD / DEVELOPMENT / CANCER / RIBOSOME BIOGENESIS
Function / homology
Function and homology information


peptidyl-lysine 3-dioxygenase activity / Protein hydroxylation / wybutosine biosynthetic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / histone H3K36 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / phospholipase A2 / tRNA binding / hydrolase activity / nucleus ...peptidyl-lysine 3-dioxygenase activity / Protein hydroxylation / wybutosine biosynthetic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / histone H3K36 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / phospholipase A2 / tRNA binding / hydrolase activity / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Cupin-like domain 8 / Cupin-like domain / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / RmlC-like jelly roll fold
Similarity search - Domain/homology
: / PYRIDINE-2,4-DICARBOXYLIC ACID / DI(HYDROXYETHYL)ETHER / GH14974p
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsChowdhury, R. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust106244/Z/14/Z United Kingdom
Citation
Journal: Sci Rep / Year: 2022
Title: Conservation of the unusual dimeric JmjC fold of JMJD7 from Drosophila melanogaster to humans.
Authors: Chowdhury, R. / Abboud, M.I. / Wiley, J. / Tumber, A. / Markolovic, S. / Schofield, C.J.
#1: Journal: Nat Chem Biol / Year: 2018
Title: The Jumonji-C oxygenase JMJD7 catalyzes (3S)-lysyl hydroxylation of TRAFAC GTPases.
Authors: Markolovic, S. / Zhuang, Q. / Wilkins, S.E. / Eaton, C.D. / Abboud, M.I. / Katz, M.J. / McNeil, H.E. / Lesniak, R.K. / Hall, C. / Struwe, W.B. / Konietzny, R. / Davis, S. / Yang, M. / Ge, W. ...Authors: Markolovic, S. / Zhuang, Q. / Wilkins, S.E. / Eaton, C.D. / Abboud, M.I. / Katz, M.J. / McNeil, H.E. / Lesniak, R.K. / Hall, C. / Struwe, W.B. / Konietzny, R. / Davis, S. / Yang, M. / Ge, W. / Benesch, J.L.P. / Kessler, B.M. / Ratcliffe, P.J. / Cockman, M.E. / Fischer, R. / Wappner, P. / Chowdhury, R. / Coleman, M.L. / Schofield, C.J.
History
DepositionFeb 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Refinement description / Category: refine_ls_restr
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GH14974p
B: GH14974p
C: GH14974p
D: GH14974p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,65826
Polymers146,8574
Non-polymers1,80122
Water3,531196
1
A: GH14974p
B: GH14974p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,47515
Polymers73,4292
Non-polymers1,04713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-33 kcal/mol
Surface area25860 Å2
MethodPISA
2
C: GH14974p
D: GH14974p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,18311
Polymers73,4292
Non-polymers7549
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-43 kcal/mol
Surface area26610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.557, 65.762, 206.957
Angle α, β, γ (deg.)90.000, 97.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
GH14974p / Jumonji domain containing 7


Mass: 36714.309 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: JMJD7, Dmel\CG10133, CG10133, Dmel_CG10133 / Plasmid: PET28A(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9VU77, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor

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Non-polymers , 5 types, 218 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PD2 / PYRIDINE-2,4-DICARBOXYLIC ACID


Mass: 167.119 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H5NO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: Sample: 16.0 mg/ml dmJMJD7 (in 50 mM Hepes-Na pH 7.5, 200 mM NaCl, 5% glycerol), 2.0 mM MnCl2 and 4.0 mM compound. Reservoir: 0.1 M Bis-Tris pH 5.4, 0.3 M magnesium chloride, 0.1 M ammonium ...Details: Sample: 16.0 mg/ml dmJMJD7 (in 50 mM Hepes-Na pH 7.5, 200 mM NaCl, 5% glycerol), 2.0 mM MnCl2 and 4.0 mM compound. Reservoir: 0.1 M Bis-Tris pH 5.4, 0.3 M magnesium chloride, 0.1 M ammonium acetate (or alternatively, 0.1 M barium chloride), and 0.002 M manganese chloride. Cryo-protection: 20% v/v ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 5, 2017 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.45→205.054 Å / Num. obs: 52754 / % possible obs: 99.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 50.1 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.062 / Rrim(I) all: 0.14 / Rsym value: 0.125 / Net I/av σ(I): 4.7 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
2.45-2.5851.776670.5520.4661.0690.958100
2.58-2.7451.872670.3570.8090.72299.9
2.74-2.934.81.968050.2420.5430.48499.9
2.93-3.1652.463650.1410.3180.28499.8
3.16-3.465458300.0830.1890.16899.9
3.46-3.875.15.753230.0570.1290.11699.7
3.87-4.4757.546850.0410.0930.08399.6
4.47-5.484.98.139700.0360.0810.07299.7
5.48-7.754.88.931020.0350.0780.0799.7
7.75-55.3544.69.617400.0280.0640.05899

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YXG

7yxg


Resolution: 2.45→55.354 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 2517 4.78 %
Rwork0.2061 50195 -
obs0.2073 52712 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.47 Å2 / Biso mean: 65.058 Å2 / Biso min: 22.42 Å2
Refinement stepCycle: final / Resolution: 2.45→55.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9702 0 210 196 10108
Biso mean--62.9 49.89 -
Num. residues----1238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610159
X-RAY DIFFRACTIONf_angle_d0.77813876
X-RAY DIFFRACTIONf_dihedral_angle_d15.6185989
X-RAY DIFFRACTIONf_chiral_restr0.051501
X-RAY DIFFRACTIONf_plane_restr0.0061817
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.45-2.49710.30091240.30322788100
2.4971-2.54810.32091240.30522810100
2.5481-2.60350.341190.29022739100
2.6035-2.66410.28771130.29222834100
2.6641-2.73070.28841500.28132777100
2.7307-2.80450.30591430.28232748100
2.8045-2.8870.35431390.29062758100
2.887-2.98020.2811550.25712782100
2.9802-3.08670.23461250.2332760100
3.0867-3.21030.26171260.21762806100
3.2103-3.35640.23611840.2192755100
3.3564-3.53330.22321360.2092787100
3.5333-3.75470.22251190.20222776100
3.7547-4.04450.20871370.17412827100
4.0445-4.45130.21591380.1657280999
4.4513-5.09510.17781580.15312764100
5.0951-6.41770.20421720.18462802100
6.4177-55.3540.20891550.19287399

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