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- PDB-6f4n: Human JMJD5 in complex with MN and 2OG. -

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Basic information

Entry
Database: PDB / ID: 6f4n
TitleHuman JMJD5 in complex with MN and 2OG.
ComponentsJmjC domain-containing protein 5
KeywordsOXIDOREDUCTASE / NON-HEME / IRON / 2-OXOGLUTARATE / DIOXYGENASE / JMJC / JMJC DOMAIN / Lysine-specific demethylase 8 / JmjC domain-containing protein 5 / Arginyl C-3 Hydroxylase / JMJD5 / KDM8 / OXYGENASE / HYPOXIA / DNA-BINDING / METAL-BINDING / TRANSLATION / DSBH / FACIAL TRIAD / CYTOPLASM / JMJC HYDROXYLASE / JMJC DEMETHYLASE / KDMS / POST-TRANSLATIONAL MODIFICATIONS / PTM / BETA-HYDROXYLATION / HYDROXYLATION / ARGININE HYDROXYLATION / RCC1 domain-containing protein 1 / RCCD1 / Regulator of chromosome condensation / 40S ribosomal protein S6 / RPS6 / RIBOSOME BIOGENESIS / TRANSCRIPTION / EPIGENETIC REGULATION / SIGNALING / DEVELOPMENT / CELL STRUCTURE / TRANSCRIPTION ACTIVATOR/INHIBITOR / PHOSPHORYLATION / CANCER / POLYMORPHISM
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 / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization / G2/M transition of mitotic cell cycle ...[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / 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
: / KDM8-like, N-terminal ARM repeats / 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 / : / Bifunctional peptidase and arginyl-hydroxylase JMJD5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.541 Å
AuthorsChowdhury, R. / Islam, M.S. / Schofield, C.J.
CitationJournal: Nat Commun / Year: 2018
Title: JMJD5 is a human arginyl C-3 hydroxylase.
Authors: Wilkins, S.E. / Islam, S. / Gannon, J.M. / Markolovic, S. / Hopkinson, R.J. / Ge, W. / Schofield, C.J. / Chowdhury, R.
History
DepositionNov 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,1196
Polymers62,7172
Non-polymers4024
Water3,405189
1
A: JmjC domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5603
Polymers31,3591
Non-polymers2012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: JmjC domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5603
Polymers31,3591
Non-polymers2012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.002, 68.002, 267.898
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 JmjC domain-containing protein 5 / LYSINE-SPECIFIC DEMETHYLASE 8 / JUMONJI DOMAIN-CONTAINING PROTEIN 5


Mass: 31358.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CATALYTIC DOMAIN (RESIDUES 153-416) / Source: (gene. exp.) Homo sapiens (human) / Gene: KDM8, JMJD5 / Plasmid: pNH-TrxT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8N371, [50S ribosomal protein L16]-arginine 3-hydroxylase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.19 Å3/Da / Density % sol: 61.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M Bis-Tris pH 6.0, 21.4 % PEG3350, 0.07 M MgCl2, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:2 ratio)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 19, 2016 / 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: 2.54→49.16 Å / Num. obs: 24683 / % possible obs: 99.9 % / Redundancy: 9.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.03 / Net I/σ(I): 25.1
Reflection shellResolution: 2.54→2.63 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2411 / CC1/2: 0.738 / Rpim(I) all: 0.423 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000706Edata reduction
HKL-2000706Edata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GJZ

4gjz


Resolution: 2.541→49.16 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.36
Details: REFINEMENT TARGET: ML and BULK SOLVENT MODELLING METHOD USED: FLAT MODEL
RfactorNum. reflection% reflection
Rfree0.2299 1242 5.05 %
Rwork0.1994 --
obs0.2009 24595 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 55.8 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.21 Å20 Å20 Å2
2--9.21 Å20 Å2
3----18.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.54 Å
Refinement stepCycle: LAST / Resolution: 2.541→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3929 0 22 189 4140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054140
X-RAY DIFFRACTIONf_angle_d0.8775658
X-RAY DIFFRACTIONf_dihedral_angle_d17.5392458
X-RAY DIFFRACTIONf_chiral_restr0.061597
X-RAY DIFFRACTIONf_plane_restr0.007742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5414-2.64320.34671200.33012503X-RAY DIFFRACTION98
2.6432-2.76350.30651420.30032512X-RAY DIFFRACTION99
2.7635-2.90910.2761610.27622526X-RAY DIFFRACTION100
2.9091-3.09140.29951190.24662596X-RAY DIFFRACTION99
3.0914-3.330.25971440.22222561X-RAY DIFFRACTION100
3.33-3.6650.20361600.20072565X-RAY DIFFRACTION100
3.665-4.19510.19211320.17442606X-RAY DIFFRACTION100
4.1951-5.28450.17071180.15452680X-RAY DIFFRACTION100
5.2845-49.17220.25671460.20052804X-RAY DIFFRACTION100

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