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- PDB-5nfn: JMJD7 IN COMPLEX WITH MN AND 2OG IN THE H32 FORM -

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Basic information

Entry
Database: PDB / ID: 5nfn
TitleJMJD7 IN COMPLEX WITH MN AND 2OG IN THE H32 FORM
ComponentsJmjC domain-containing protein 7
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 (3S)-dioxygenase / protein hydroxylation / peptidyl-lysine 3-dioxygenase activity / 2-oxoglutarate-dependent dioxygenase activity / Hydrolases; Acting on peptide bonds (peptidases) / aminopeptidase activity / monooxygenase activity / methylated histone binding / endopeptidase activity / proteolysis ...peptidyl-lysine (3S)-dioxygenase / protein hydroxylation / peptidyl-lysine 3-dioxygenase activity / 2-oxoglutarate-dependent dioxygenase activity / Hydrolases; Acting on peptide bonds (peptidases) / aminopeptidase activity / monooxygenase activity / methylated histone binding / endopeptidase activity / proteolysis / 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. / Jelly Rolls / JmjC domain / JmjC domain profile. / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / NITRATE ION / Bifunctional peptidase and (3S)-lysyl hydroxylase JMJD7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.982 Å
AuthorsChowdhury, R. / Markolovic, S. / Schofield, C.J.
CitationJournal: To Be Published
Title: (3S)-Lysyl hydroxylation of TRAFAC GTPases is catalyzed by the human Jumonji-C oxygenase JMJD7.
Authors: Markolovic, S. / Zhuang, Q. / Wilkins, S.E. / Eaton, C. / Katz, M.J. / Smith, H.E. / Lesniak, R.K. / Hall, C. / Struwe, W.B. / Konietzny, R. / Davis, S. / Yang, M. / Ge, W. / Benesch, J.L. / ...Authors: Markolovic, S. / Zhuang, Q. / Wilkins, S.E. / Eaton, C. / Katz, M.J. / Smith, H.E. / Lesniak, R.K. / Hall, C. / Struwe, W.B. / Konietzny, R. / Davis, S. / Yang, M. / Ge, W. / Benesch, J.L. / Kessler, B.M. / Ratcliffe, P.J. / Cockman, M.E. / Fischer, R. / Wappner, P. / Chowdhury, R. / Coleman, M.L. / Schofield, C.J.
History
DepositionMar 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: JmjC domain-containing protein 7
B: JmjC domain-containing protein 7
C: JmjC domain-containing protein 7
D: JmjC domain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,49322
Polymers152,0334
Non-polymers1,46018
Water4,540252
1
A: JmjC domain-containing protein 7
B: JmjC domain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,81911
Polymers76,0162
Non-polymers8029
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-51 kcal/mol
Surface area25650 Å2
MethodPISA
2
C: JmjC domain-containing protein 7
D: JmjC domain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,67411
Polymers76,0162
Non-polymers6589
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-48 kcal/mol
Surface area25810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.220, 207.220, 211.788
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
JmjC domain-containing protein 7 / Jumonji domain-containing protein 7


Mass: 38008.129 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD7 / Plasmid: PET28A(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: P0C870

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Non-polymers , 5 types, 270 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-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 3.04 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 25 mg/mL His6-JMJD7, 2 mM MnCl2, 4 mM 2OG, 1.5 M Sodium Nitrate, 0.1 M Sodium Acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 11, 2014 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.98→48.459 Å / Num. obs: 35671 / % possible obs: 100 % / Redundancy: 15 % / Biso Wilson estimate: 75.2 Å2 / Rmerge(I) obs: 0.169 / Net I/σ(I): 10.3
Reflection shellResolution: 2.98→3.07 Å / Redundancy: 14.9 % / Rmerge(I) obs: 1.296 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000706Edata reduction
HKL-2000706Edata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.982→48.459 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2508 1720 4.85 %
Rwork0.2489 --
obs0.24 35437 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.4 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 110 Å2
Baniso -1Baniso -2Baniso -3
1-28.54 Å20 Å20 Å2
2--28.54 Å20 Å2
3----57.09 Å2
Refinement stepCycle: LAST / Resolution: 2.982→48.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9998 0 86 252 10336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110446
X-RAY DIFFRACTIONf_angle_d1.4514304
X-RAY DIFFRACTIONf_dihedral_angle_d14.4656185
X-RAY DIFFRACTIONf_chiral_restr0.0781529
X-RAY DIFFRACTIONf_plane_restr0.0081866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9824-3.07010.47371530.43872753X-RAY DIFFRACTION99
3.0701-3.16920.41931390.40562790X-RAY DIFFRACTION99
3.1692-3.28240.40791260.35512804X-RAY DIFFRACTION99
3.2824-3.41380.35151330.31342809X-RAY DIFFRACTION99
3.4138-3.56910.3451440.28462778X-RAY DIFFRACTION99
3.5691-3.75720.27341450.2512788X-RAY DIFFRACTION99
3.7572-3.99250.26061450.22672788X-RAY DIFFRACTION99
3.9925-4.30060.25721400.20722817X-RAY DIFFRACTION100
4.3006-4.73310.20561480.18212824X-RAY DIFFRACTION100
4.7331-5.41720.22731500.18982832X-RAY DIFFRACTION100
5.4172-6.82210.23831530.22552830X-RAY DIFFRACTION100
6.8221-48.4590.21031440.22212902X-RAY DIFFRACTION98

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