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1h0o

Cobalt substitution of mouse R2 ribonucleotide reductase to model the reactive diferrous state

Method: X-RAY DIFFRACTION Dmax: 67.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE

MUS MUSCULUS

UniProt P11157

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 1–390 Not recorded CO COBALT (II) ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.7；0.1 M NA-ACETATE BUFFER PH4.7, 1.2 M NACL, 7.5 MG/ML APO-R2 PROTEIN. CRYSTALS WERE MADE BY CO-CRYSTALLISATION (3.8 EQV. CO2+)., pH 4.70 Resolution 2.20 Å R-free 0.282

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 1H0O Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AFT SMALL SUBUNIT C-TERMINAL INHIBITORY PEPTIDE OF MOUSE RIBONUCLEOTIDE REDUCTASE AS BOUND TO THE LARGE SUBUNIT, NMR, 26 STRUCTURES Deposited 1997-03-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 384–390（7 aa） Fragment：C-TERMINAL RESIDUES AC-FTLDADF OF SMALL SUBUNIT
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；287 K
Resolution not provided
1H0N Cobalt substitution of mouse R2 ribonucleotide reductase to model the reactive diferrous state Deposited 2002-06-26 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–390（390 aa）
Not recorded CO COBALT (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；0.1 M NA-ACETATE BUFFER PH4.7, 1.2 M NACL, 7.5 MG/ML APO-R2 PROTEIN. CRYSTALS WERE SOAKED IN 5 MM CO2+ SOLUTION, PH INCREASED TO 6
Resolution 2.40 Å R-free 0.297
1W68 Crystal Structure of Mouse Ribonucleotide Reductase Subunit R2 under Oxidizing Conditions. A Fully Occupied Dinuclear Iron Cluster. Deposited 2004-08-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–390（390 aa）
Not recorded FEO MU-OXO-DIIRON × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；0.1 M SODIUM ACETATE PH 4.7, 1.2 M SODIUM CHLORIDE
Resolution 2.20 Å R-free 0.260
1W69 Crystal Structure of Mouse Ribonucleotide Reductase Subunit R2 under Reducing Conditions. A Fully Occupied Dinuclear Iron Cluster and Bound Acetate. Deposited 2004-08-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–390（390 aa）
Not recorded FE2 FE (II) ION × 4 ACY ACETIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；0.1 M SODIUM ACETATE PH 4.7, 1.2 M SODIUM CHLORIDE
Resolution 2.20 Å R-free 0.272
1XSM PROTEIN R2 OF RIBONUCLEOTIDE REDUCTASE FROM MOUSE Deposited 1996-07-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–390（390 aa）
Not recorded FE FE (III) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.7；1.0-1.2 M NACL, 0.1 M SODIUM ACETATE, PH 4.7, 0-4% PEG4000.
Resolution 2.30 Å R-free 0.250

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RIR2_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–390； UniProt 1–390

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 1h0o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1h0o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1h0o
Deposition date deposition_date2002-06-26
Structure title titleCobalt substitution of mouse R2 ribonucleotide reductase to model the reactive diferrous state
Keywords keywordsOXIDOREDUCTASE, RIBONUCLEOTIDE REDUCTASE, DINUCLEAR METAL-CLUSTER; 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_guinier20.40 Å
Radius of gyration Rg (electron density) rg_electron19.41 Å
Forward intensity I(0) i018576200.00
Molecular weight molecular_weight33792.0 kDa
Excluded volume excluded_volume42616 ų
Envelope volume envelope_volume47923 ų
Hydration-shell volume shell_volume20592 ų
Envelope diameter envelope_diameter70.8 Å
Shell Rg shell_rg25.94 Å
Envelope Rg envelope_rg19.80 Å
Shape Rg shape_rg19.41 Å
Total Rg total_rg20.30 Å
Total atoms total_atoms2381
Residues n_residues288
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 dmax67.4 Å
Rg (real space) rg_real20.36 Å
Rg uncertainty (real space) rg_real_error0.40 Å
I(0) (real space) i0_real1.8580e+07
I(0) uncertainty (real space) i0_real_error2.3220e+05
Rg (reciprocal space) rg_reciprocal20.36 Å
I(0) (reciprocal space) i0_reciprocal18580000.0000
Solution quality estimate total_estimate0.8003
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary25.0 Å
Skewness Skewness skewness0.329
Kurtosis Kurtosis kurtosis-0.224
Angular range angular_range— – 0.3900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5149000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.800; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1h0oa_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.2 — Ribonucleotide reductase-like

CATH v4.4 (1 domains)

Domain ID domain_id1h0oA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology620 — Ribonucleotide Reductase, subunit A
Homologous superfamily homologous superfamily20 — Ribonucleotide Reductase, subunit A
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8. Citations (1)

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9. Files and Curves (10)