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4bu2

60S ribosomal protein L27A histidine hydroxylase (MINA53) in complex with Ni(II) and 2-oxoglutarate (2OG)

Method: X-RAY DIFFRACTION Dmax: 78.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE MINA

HOMO SAPIENS

UniProt Q8IUF8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 26–465 Fragment：CATALYTIC DOMAIN, RESIDUES 26-465 Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) NI NICKEL (II) ION × 4 AKG 2-OXOGLUTARIC ACID × 2 EDO 1,2-ETHANEDIOL × 8 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；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 Resolution 2.78 Å R-free 0.233

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4BU2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2XDV Crystal Structure of the Catalytic Domain of FLJ14393 Deposited 2010-05-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 26–465（440 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 26-465
Not recorded OGA N-OXALYLGLYCINE × 6 NI NICKEL (II) ION × 36 MN MANGANESE (II) ION × 6 EDO 1,2-ETHANEDIOL × 12 CD CADMIUM ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions 12% PEG 3350; 0.005M COCL2; 0.005M MGCL2; 0.005M CDCL2; 0.005M NICL2; 0.1M HEPES PH 7.5
Resolution 2.57 Å R-free 0.229
2XDV Crystal Structure of the Catalytic Domain of FLJ14393 Deposited 2010-05-07 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–465（440 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 26-465
Not recorded OGA N-OXALYLGLYCINE × 2 NI NICKEL (II) ION × 12 MN MANGANESE (II) ION × 2 EDO 1,2-ETHANEDIOL × 4 CD CADMIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions 12% PEG 3350; 0.005M COCL2; 0.005M MGCL2; 0.005M CDCL2; 0.005M NICL2; 0.1M HEPES PH 7.5
Resolution 2.57 Å R-free 0.229
4BXF 60S ribosomal protein L27A histidine hydroxylase (MINA53 Y209C) in complex with MN(II), 2-oxoglutarate (2OG) and 60S ribosomal protein L27A (RPL27A G37C) peptide fragment Deposited 2013-07-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 26–465（440 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 26-465
Chain B 26–465（440 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 26-465
Mutation：YES Mutation：YES MN MANGANESE (II) ION × 2 AKG 2-OXOGLUTARIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；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
Resolution 2.05 Å R-free 0.221

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MINA_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–442； UniProt 26–465

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4bu2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4bu2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4bu2
Deposition date deposition_date2013-06-19
Structure title title60S ribosomal protein L27A histidine hydroxylase (MINA53) in complex with Ni(II) and 2-oxoglutarate (2OG)
Keywords keywords;OXIDOREDUCTASE, NON-HEME, IRON-BINDING, DSBH, 2-OXOGLUTARATE, DIOXYGENASE, JMJC DOMAIN, RIBOSOME BIOGENESIS, NUCLEAR PROTEIN, RPL27A, BETA-HYDROXYLATION, TRANSCRIPTION AND EPIGENETIC REGULATION, SIGNALING ;; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.42 Å
Radius of gyration Rg (electron density) rg_electron24.64 Å
Forward intensity I(0) i031154200.00
Molecular weight molecular_weight43421.0 kDa
Excluded volume excluded_volume54452 ų
Envelope volume envelope_volume70753 ų
Hydration-shell volume shell_volume24529 ų
Envelope diameter envelope_diameter83.6 Å
Shell Rg shell_rg31.17 Å
Envelope Rg envelope_rg25.02 Å
Shape Rg shape_rg24.62 Å
Total Rg total_rg25.53 Å
Total atoms total_atoms3040
Residues n_residues373
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax78.8 Å
Rg (real space) rg_real25.43 Å
Rg uncertainty (real space) rg_real_error0.48 Å
I(0) (real space) i0_real3.1150e+07
I(0) uncertainty (real space) i0_real_error4.0480e+05
Rg (reciprocal space) rg_reciprocal25.43 Å
I(0) (reciprocal space) i0_reciprocal31150000.0000
Solution quality estimate total_estimate0.9089
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.7 Å
Skewness Skewness skewness0.296
Kurtosis Kurtosis kurtosis-0.601
Angular range angular_range— – 0.3100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3163000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.971
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id4bu2A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily650 — Cupin
Domain ID domain_id4bu2A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily1500 — JmjC domain-containing ribosomal oxygenase (ROX), dimer domain
Domain ID domain_id4bu2A03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily40 —
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8. Citations (2)

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9. Files and Curves (10)