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- PDB-4bxf: 60S ribosomal protein L27A histidine hydroxylase (MINA53 Y209C) i... -

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Entry
Database: PDB / ID: 4bxf
Title60S ribosomal protein L27A histidine hydroxylase (MINA53 Y209C) in complex with MN(II), 2-oxoglutarate (2OG) and 60S ribosomal protein L27A (RPL27A G37C) peptide fragment
Components
  • 60S RIBOSOMAL PROTEIN L27A
  • BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE MINA
KeywordsOXIDOREDUCTASE/TRANSLATION / OXIDOREDUCTASE-TRANSLATION COMPLEX / OXIDOREDUCTASE / NON-HEME / IRON-BINDING / DSBH / DIOXYGENASE / JMJC DOMAIN / RIBOSOME BIOGENESIS / NUCLEAR PROTEIN / BETA-HYDROXYLATION / TRANSCRIPTION AND EPIGENETIC REGULATION / SIGNALING
Function / homologyRibosomal protein L18e/L15P / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L18e/L15P superfamily / Ribosomal protein L15 / JmjC domain / Ribosomal protein L15, conserved site / Cupin superfamily protein / Ribosomal protein L15 signature. / JmjC domain profile. / L13a-mediated translational silencing of Ceruloplasmin expression ...Ribosomal protein L18e/L15P / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L18e/L15P superfamily / Ribosomal protein L15 / JmjC domain / Ribosomal protein L15, conserved site / Cupin superfamily protein / Ribosomal protein L15 signature. / JmjC domain profile. / L13a-mediated translational silencing of Ceruloplasmin expression / Peptide chain elongation / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Selenocysteine synthesis / HDMs demethylate histones / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Eukaryotic Translation Termination / Regulation of expression of SLITs and ROBOs / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / JmjC domain-containing / SRP-dependent cotranslational protein targeting to membrane / translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / 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 demethylase activity / dioxygenase activity / ribosome biogenesis / cytosolic large ribosomal subunit / transcription factor complex / structural constituent of ribosome / translation / nucleolus / endoplasmic reticulum / RNA binding / membrane / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / 60S ribosomal protein L27a / Ribosomal oxygenase 2
Function and homology information
Specimen sourceHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.05 Å resolution
AuthorsChowdhury, R. / 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.S. / Kavanagh, K.L. / von Delft, F. / Oppermann, U. / McDonough, M.A. / Doherty, A.J. / Schofield, C.J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 10, 2013 / Release: May 14, 2014
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 14, 2014Structure modelrepositoryInitial release
1.1May 21, 2014Structure modelDatabase references
1.2Jun 25, 2014Structure modelDatabase references
1.3Feb 21, 2018Structure modelDatabase referencescitation / citation_author_citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
1.4Jan 30, 2019Structure modelData collection / Experimental preparationdatabase_PDB_rev / database_PDB_rev_record / exptl_crystal_grow_exptl_crystal_grow.method / _exptl_crystal_grow.temp

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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 MINA
B: BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE MINA
C: 60S RIBOSOMAL PROTEIN L27A
D: 60S RIBOSOMAL PROTEIN L27A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7068
Polyers105,3044
Non-polymers4024
Water5,981332
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)10890
ΔGint (kcal/M)-76.7
Surface area (Å2)35840
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)70.340, 88.390, 167.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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


Mass: 50372.215 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 26-465 / Mutation: YES / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
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: Protein/peptide 60S RIBOSOMAL PROTEIN L27A /


Mass: 2279.565 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-50 / Mutation: YES / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P46776
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Formula: Mn / Manganese
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Formula: C5H6O5 / Alpha-Ketoglutaric acid
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Formula: H2O / Water

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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: 2.54 / Density percent sol: 51.66 % / Description: NONE
Crystal growTemp: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: VAPOR DIFFUSION SITTING DROP. 0.1M BIS-TRIS PROPANE PH 8.5, 0.02M NA-K-PHOSPHATE, 20-22% (W/V) PEG 3350, 0.002 M MNCL2, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Details: MIRRORS / Detector: PIXEL / Collection date: Mar 16, 2013
RadiationMonochromator: SI 111 / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 31.2 Å2 / D resolution high: 2.05 Å / D resolution low: 64.83 Å / Number obs: 64784 / Observed criterion sigma I: 2 / Rmerge I obs: 0.11 / NetI over sigmaI: 7 / Redundancy: 3.3 % / Percent possible obs: 98.2
Reflection shellRmerge I obs: 0.9 / Highest resolution: 2.05 Å / Lowest resolution: 2.16 Å / MeanI over sigI obs: 2 / Redundancy: 3.4 % / Percent possible all: 97.3

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Processing

Software
NameVersionClassification
CNS1.3refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BU2
Details: BULK SOLVENT MODEL USED / R Free selection details: RANDOM / Data cutoff high absF: 298958.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 61.7167 / Solvent model param ksol: 0.4
Displacement parametersB iso mean: 40.7 Å2 / Aniso B11: 6.57 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: -1.7 Å2 / Aniso B23: 0 Å2 / Aniso B33: -4.87 Å2
Least-squares processR factor R free: 0.221 / R factor R free error: 0.002 / R factor R work: 0.22 / R factor obs: 0.22 / Highest resolution: 2.05 Å / Lowest resolution: 64.83 Å / Number reflection R free: 3310 / Number reflection obs: 64784 / Percent reflection R free: 5.1 / Percent reflection obs: 98.2
Refine analyzeLuzzati coordinate error free: 0.29 Å / Luzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.38 Å / Luzzati sigma a obs: 0.39 Å
Refine hist #LASTHighest resolution: 2.05 Å / Lowest resolution: 64.83 Å
Number of atoms included #LASTProtein: 6723 / Nucleic acid: 0 / Ligand: 22 / Solvent: 332 / Total: 7077
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.0
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints ncsNcs model details: NONE
Refine LS shellHighest resolution: 2.05 Å / R factor R free: 0.329 / R factor R free error: 0.01 / R factor R work: 0.309 / Lowest resolution: 2.16 Å / Number reflection R free: 510 / Number reflection R work: 9275 / Total number of bins used: 7 / Percent reflection R free: 5.5 / Percent reflection obs: 97.3
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 DIFFRACTION42OG.PAR2OG.TOP

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