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- PDB-4bu2: 60S ribosomal protein L27A histidine hydroxylase (MINA53) in comp... -

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Basic information

Entry
Database: PDB / ID: 4bu2
Title60S ribosomal protein L27A histidine hydroxylase (MINA53) in complex with Ni(II) and 2-oxoglutarate (2OG)
ComponentsBIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE MINA
KeywordsOXIDOREDUCTASE / NON-HEME / IRON-BINDING / DSBH / 2-OXOGLUTARATE / DIOXYGENASE / JMJC DOMAIN / RIBOSOME BIOGENESIS / NUCLEAR PROTEIN / RPL27A / BETA-HYDROXYLATION / TRANSCRIPTION AND EPIGENETIC REGULATION / SIGNALING
Function / homology
Function and homology information


protein-L-histidine (3S)-3-hydroxylase / peptidyl-histidine dioxygenase activity / histone H3K36 demethylase activity / histone H3K4 demethylase activity / Protein hydroxylation / histone demethylase activity / HDMs demethylate histones / transcription corepressor activity / ribosome biogenesis / transcription regulator complex ...protein-L-histidine (3S)-3-hydroxylase / peptidyl-histidine dioxygenase activity / histone H3K36 demethylase activity / histone H3K4 demethylase activity / Protein hydroxylation / histone demethylase activity / HDMs demethylate histones / transcription corepressor activity / ribosome biogenesis / transcription regulator complex / nucleolus / nucleoplasm / metal ion binding / identical protein binding / cytosol
Similarity search - Function
ROXA-like, winged helix / ROXA-like winged helix / 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. ...ROXA-like, winged helix / ROXA-like winged helix / 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
2-OXOGLUTARIC ACID / NICKEL (II) ION / Ribosomal oxygenase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.78 Å
AuthorsChowdhury, R. / Clifton, I.J. / McDonough, M.A. / Ng, S.S. / Pilka, E. / Oppermann, U. / Schofield, C.J.
Citation
Journal: Nature / Year: 2014
Title: Ribosomal oxygenases are structurally conserved from prokaryotes to humans.
Authors: Chowdhury, R. / Sekirnik, R. / Brissett, N.C. / Krojer, T. / Ho, C.H. / Ng, S.S. / Clifton, I.J. / Ge, W. / Kershaw, N.J. / Fox, G.C. / Muniz, J.R.C. / Vollmar, M. / Phillips, C. / Pilka, E. ...Authors: Chowdhury, R. / Sekirnik, R. / Brissett, N.C. / Krojer, T. / Ho, C.H. / Ng, S.S. / Clifton, I.J. / Ge, W. / Kershaw, N.J. / Fox, G.C. / Muniz, J.R.C. / Vollmar, M. / Phillips, C. / Pilka, E.S. / Kavanagh, K.L. / von Delft, F. / Oppermann, U. / McDonough, M.A. / Doherty, A.J. / Schofield, C.J.
#1: Journal: Nat.Chem.Biol. / Year: 2012
Title: Oxygenase-Catalyzed Ribosome Hydroxylation Occurs in Prokaryotes and Humans.
Authors: Ge, W. / Wolf, A. / Feng, T. / Ho, C. / Sekirnik, R. / Zayer, A. / Granatino, N. / Cockman, M.E. / Loenarz, C. / Loik, N.D. / Hardy, A.P. / Claridge, T.D.W. / Hamed, R.B. / Chowdhury, R. / ...Authors: Ge, W. / Wolf, A. / Feng, T. / Ho, C. / Sekirnik, R. / Zayer, A. / Granatino, N. / Cockman, M.E. / Loenarz, C. / Loik, N.D. / Hardy, A.P. / Claridge, T.D.W. / Hamed, R.B. / Chowdhury, R. / Gong, L. / Robinson, C.V. / Trudgian, D.C. / Jiang, M. / Mackeen, M.M. / Mccullagh, J.S. / Gordiyenko, Y. / Thalhammer, A. / Yamamoto, A. / Yang, M. / Liu-Yi, P. / Zhang, Z. / Schmidt-Zachmann, M. / Kessler, B.M. / Ratcliffe, P.J. / Preston, G.M. / Coleman, M.L. / Schofield, C.J.
History
DepositionJun 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Jun 25, 2014Group: Database references
Revision 1.3Feb 21, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_id_ISSN ..._audit_author.name / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE MINA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3498
Polymers50,8371
Non-polymers5127
Water2,198122
1
A: BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE MINA
hetero molecules

A: BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE MINA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,69816
Polymers101,6752
Non-polymers1,02414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_555-y+1/4,-x+1/4,-z+1/41
Buried area9790 Å2
ΔGint-62 kcal/mol
Surface area32920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.632, 184.632, 184.632
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE MINA / 60S RIBOSOMAL PROTEIN L27A HISTIDINE HYDROXYLASE MINA / HISTONE RPL27A HISTIDINE HYDROXYLASE MINA / ...60S RIBOSOMAL PROTEIN L27A HISTIDINE HYDROXYLASE MINA / HISTONE RPL27A HISTIDINE HYDROXYLASE MINA / LYSINE DEMETHYLASE MINA / MYC-INDUCED NUCLEAR ANTIGEN / MINERAL DUST-INDUCED GENE PROTEIN / NUCLEOLAR PROTEIN 52 / RIBOSOMAL OXYGENASE MINA / ROX


Mass: 50837.426 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 26-465 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2
References: UniProt: Q8IUF8, 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
#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.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 5.14 Å3/Da / Density % sol: 76.1 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M BIS-TRIS PROPANE PH 6.5, 19-22% (W/V) PEG 3350, 0.2M AMMONIUM SULPHATE, 0.005M NICL2, TEMPERATURE 293K. VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9699
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2007 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9699 Å / Relative weight: 1
ReflectionResolution: 2.78→37.69 Å / Num. obs: 27690 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 40.7 % / Biso Wilson estimate: 55.2 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 20.4
Reflection shellResolution: 2.78→2.93 Å / Redundancy: 42 % / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.3refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.78→37.69 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 115409.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1496 5.4 %RANDOM
Rwork0.228 ---
obs0.228 27690 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.0245 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 57.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.78→37.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 28 122 3162
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it1.622
X-RAY DIFFRACTIONc_scangle_it2.572.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.78→2.93 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.346 191 4.8 %
Rwork0.315 3970 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4AKG.PARAKG.TOP
X-RAY DIFFRACTION5EDO.PAREDO.TOP

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