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- PDB-3uyj: Crystal structure of JMJD5 catalytic core domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3uyj
TitleCrystal structure of JMJD5 catalytic core domain in complex with nickle and alpha-KG
ComponentsLysine-specific demethylase 8
KeywordsOXIDOREDUCTASE / jellyroll-like all beta fold / Demethylase / Nuclear
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 / NICKEL (II) ION / Bifunctional peptidase and arginyl-hydroxylase JMJD5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.351 Å
AuthorsSu, X. / Li, H.
CitationJournal: To be Published
Title: Crystal structure of JMJD5 catalytic core domain in complex with nickle and alpha-KG
Authors: Su, X. / Li, H.
History
DepositionDec 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)57,7776
Polymers57,3672
Non-polymers4104
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-26 kcal/mol
Surface area22170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.393, 68.393, 266.686
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-containing demethylase / JmjC domain-containing protein 5 / Jumonji domain-containing protein 5


Mass: 28683.609 Da / Num. of mol.: 2 / Fragment: Catalytic core domain, UNP residues 173-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD5, KDM8 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta2(DE3)
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-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.: 209 / 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: 3.14 Å3/Da / Density % sol: 60.81 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7.5
Details: 8% PEG3350, 0.1M HepesNa pH 7.5, EVAPORATION, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2011 / Details: mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. all: 31174 / Num. obs: 30809 / % possible obs: 98.83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 42.86 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 22.6
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.335 / % possible all: 99

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.351→19.994 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / σ(F): 0 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2531 1564 5.08 %
Rwork0.2029 --
obs0.2054 30809 98.83 %
all-31174 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.602 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.4271 Å2-0 Å2-0 Å2
2--6.4271 Å20 Å2
3----12.8543 Å2
Refinement stepCycle: LAST / Resolution: 2.351→19.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3837 0 22 209 4068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133989
X-RAY DIFFRACTIONf_angle_d1.0585446
X-RAY DIFFRACTIONf_dihedral_angle_d16.6111480
X-RAY DIFFRACTIONf_chiral_restr0.078567
X-RAY DIFFRACTIONf_plane_restr0.006706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3505-2.43440.31721570.23382888X-RAY DIFFRACTION100
2.4344-2.53170.32041440.23782906X-RAY DIFFRACTION100
2.5317-2.64660.31111710.22632864X-RAY DIFFRACTION100
2.6466-2.78580.26341690.21972879X-RAY DIFFRACTION100
2.7858-2.95990.30381440.21782969X-RAY DIFFRACTION100
2.9599-3.18750.27581380.22052928X-RAY DIFFRACTION100
3.1875-3.50680.241560.20812944X-RAY DIFFRACTION100
3.5068-4.01060.23281600.19842868X-RAY DIFFRACTION96
4.0106-5.03960.21971580.1632895X-RAY DIFFRACTION96
5.0396-19.99470.24791670.20863104X-RAY DIFFRACTION98

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