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- PDB-4y4r: Crystal structure of ribosomal oxygenase NO66 dimer mutant -

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Basic information

Entry
Database: PDB / ID: 4y4r
TitleCrystal structure of ribosomal oxygenase NO66 dimer mutant
ComponentsBifunctional lysine-specific demethylase and histidyl-hydroxylase NO66
KeywordsOXIDOREDUCTASE / ribosomal oxygenase / NO66 / Dimer mutant
Function / homology
Function and homology information


protein-L-histidine (3S)-3-hydroxylase / protein demethylase activity / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / peptidyl-histidine dioxygenase activity / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / histone H3K36 demethylase activity / histone H3K4 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / Protein hydroxylation ...protein-L-histidine (3S)-3-hydroxylase / protein demethylase activity / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / peptidyl-histidine dioxygenase activity / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / histone H3K36 demethylase activity / histone H3K4 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / Protein hydroxylation / negative regulation of osteoblast differentiation / iron ion binding / negative regulation of DNA-templated transcription / nucleolus / nucleoplasm / nucleus
Similarity search - Function
: / Ribosomal oxygenase 1, C-terminal winged helix domain / JmjC domain-containing ribosomal oxygenase (ROX), dimer domain / Outer Surface Protein A; domain 3 - #40 / JmjC domain-containing / JmjC domain / Outer Surface Protein A; domain 3 / Cupin / JmjC domain / JmjC domain profile. ...: / Ribosomal oxygenase 1, C-terminal winged helix domain / JmjC domain-containing ribosomal oxygenase (ROX), dimer domain / Outer Surface Protein A; domain 3 - #40 / JmjC domain-containing / JmjC domain / Outer Surface Protein A; domain 3 / Cupin / JmjC domain / JmjC domain profile. / Arc Repressor Mutant, subunit A / Jelly Rolls / Alpha-Beta Complex / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / NICKEL (II) ION / Ribosomal oxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsWang, C. / Hang, T. / Zang, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of the JmjC domain-containing protein NO66 complexed with ribosomal protein Rpl8.
Authors: Wang, C. / Zhang, Q. / Hang, T. / Tao, Y. / Ma, X. / Wu, M. / Zhang, X. / Zang, J.
History
DepositionFeb 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66
B: Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3075
Polymers103,1302
Non-polymers1763
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-66 kcal/mol
Surface area37240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.060, 144.210, 144.210
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 Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66 / 60S ribosomal protein L8 histidine hydroxylase / Histone lysine demethylase NO66 / Myc-associated ...60S ribosomal protein L8 histidine hydroxylase / Histone lysine demethylase NO66 / Myc-associated protein with JmjC domain / Nucleolar protein 66 / hsNO66 / Ribosomal oxygenase NO66 / ROX


Mass: 51565.191 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 176-525, 541-641
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NO66, C14orf169, MAPJD / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H6W3, 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 ...References: UniProt: Q9H6W3, 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 H3]-dimethyl-L-lysine36 demethylase
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.34 Å3/Da / Density % sol: 71.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 1.0M ammonium monohydric phosphate, 0.1M acetate pH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.3→64.58 Å / Num. obs: 27284 / % possible obs: 98.8 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 12.4
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 3 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata processing
PHASERphasing
Cootmodel building
RefinementResolution: 3.3→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.884 / SU B: 23.085 / SU ML: 0.373 / Cross valid method: THROUGHOUT / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27096 1372 5 %RANDOM
Rwork0.21708 ---
obs0.21973 25870 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.441 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å2-0 Å2
2---1.08 Å20 Å2
3---2.06 Å2
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7072 0 6 4 7082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197258
X-RAY DIFFRACTIONr_bond_other_d0.0050.026758
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9649875
X-RAY DIFFRACTIONr_angle_other_deg0.848315474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8785885
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86722.865363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.54151140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3041572
X-RAY DIFFRACTIONr_chiral_restr0.080.21066
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218303
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021769
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.9469.893553
X-RAY DIFFRACTIONr_mcbond_other6.9489.8893551
X-RAY DIFFRACTIONr_mcangle_it10.47514.8294433
X-RAY DIFFRACTIONr_mcangle_other10.47414.8314434
X-RAY DIFFRACTIONr_scbond_it7.11710.2193705
X-RAY DIFFRACTIONr_scbond_other7.11610.2173706
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.91915.1835443
X-RAY DIFFRACTIONr_long_range_B_refined13.87178.0088199
X-RAY DIFFRACTIONr_long_range_B_other13.87178.038193
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 104 -
Rwork0.292 1811 -
obs--97.31 %

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