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9zmx

Crystal structure of an Iole protein from Brucella melitensis (cobalt complex)

Method: X-RAY DIFFRACTION Dmax: 55.4 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Iole protein

Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)

UniProt Q8YCG0

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–299 Not recorded CO COBALT (II) ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；crystal screen C4: 0.2M Na acetate, 0.1M Na cacodylate pH 6.5, 30% PEG 8000. BrmeA.18154.a.B2.PW39413 at 8 mg/mL. Overnight soak in 20mM Cobalt Chloride. plate 20331 C4 drop 1, Puck: PSL-0704, Cryo: direct Resolution 2.30 Å R-free 0.242

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 9ZMX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9ZMU Crystal structure of an Iole protein from Brucella melitensis (hexagonal P form) Deposited 2025-12-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–299（299 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；MPH D1: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Imidazole/MES, pH 6.5, 20 mM 1,6-Hexanediol, 20 mM 1-Butanol, 20 mM 1,2-Propanediol, 20 mM 2-Propanol, 20 mM 1,4-Butanediol and 20 mM 1,3-Propanediol. BrmeA.18154.a.B2.PW39413 at 8 mg/mL. plate 20332 D1 drop 1, Puck: PSL-0613, Cryo: direct
Resolution 1.98 Å R-free 0.294
9ZMV Crystal structure of an Iole protein from Brucella melitensis (orthorhombic P form) Deposited 2025-12-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–299（299 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；MPH D1: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Imidazole/MES, pH 6.5, 20 mM 1,6-Hexanediol, 20 mM 1-Butanol, 20 mM 1,2-Propanediol, 20 mM 2-Propanol, 20 mM 1,4-Butanediol and 20 mM 1,3-Propanediol. BrmeA.18154.a.B2.PW39413 at 8 mg/mL. plate 20332 D1 drop 1, Puck: PSL-0614, Cryo: direct
Resolution 2.10 Å R-free 0.228
9ZMW Crystal structure of a Iole protein from Brucella melitensis (orthorhombic P form 2) Deposited 2025-12-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–299（299 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；crystal screen C4: 0.2M Na acetate, 0.1M Na cacodylate pH 6.5, 30% PEG 8000. BrmeA.18154.a.B2.PW39413 at 8 mg/mL. plate 20331 C4 drop 1, Puck: PSL-0701, Cryo: direct
Resolution 2.30 Å R-free 0.235
9ZMW Crystal structure of a Iole protein from Brucella melitensis (orthorhombic P form 2) Deposited 2025-12-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–299（299 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；crystal screen C4: 0.2M Na acetate, 0.1M Na cacodylate pH 6.5, 30% PEG 8000. BrmeA.18154.a.B2.PW39413 at 8 mg/mL. plate 20331 C4 drop 1, Puck: PSL-0701, Cryo: direct
Resolution 2.30 Å R-free 0.235
9ZMW Crystal structure of a Iole protein from Brucella melitensis (orthorhombic P form 2) Deposited 2025-12-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–299（299 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；crystal screen C4: 0.2M Na acetate, 0.1M Na cacodylate pH 6.5, 30% PEG 8000. BrmeA.18154.a.B2.PW39413 at 8 mg/mL. plate 20331 C4 drop 1, Puck: PSL-0701, Cryo: direct
Resolution 2.30 Å R-free 0.235

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

View Construct and Data Evidence
UniProt name Q8YCG0_BRUME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 9–307； UniProt 1–299

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 9zmx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9zmx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9zmx
Deposition date deposition_date2025-12-11
最后修订 last_revision2025-12-24
Structure title titleCrystal structure of an Iole protein from Brucella melitensis (cobalt complex)
Keywords keywordsSSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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_guinier19.11 Å
Radius of gyration Rg (electron density) rg_electron17.93 Å
Forward intensity I(0) i019735800.00
Molecular weight molecular_weight33140.0 kDa
Excluded volume excluded_volume41145 ų
Envelope volume envelope_volume45924 ų
Hydration-shell volume shell_volume20706 ų
Envelope diameter envelope_diameter55.1 Å
Shell Rg shell_rg24.77 Å
Envelope Rg envelope_rg18.10 Å
Shape Rg shape_rg17.93 Å
Total Rg total_rg18.85 Å
Total atoms total_atoms2328
Residues n_residues299
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 dmax55.4 Å
Rg (real space) rg_real18.93 Å
Rg uncertainty (real space) rg_real_error0.23 Å
I(0) (real space) i0_real1.9740e+07
I(0) uncertainty (real space) i0_real_error2.1130e+05
Rg (reciprocal space) rg_reciprocal18.96 Å
I(0) (reciprocal space) i0_reciprocal19740000.0000
Solution quality estimate total_estimate0.7208
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.9 Å
Skewness Skewness skewness0.017
Kurtosis Kurtosis kurtosis-0.576
Angular range angular_range— – 0.4150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7370000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 0.182; Positv: 1.000; Valcen: 0.968; Smooth: 0.997
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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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8. Citations (1)

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9. Files and Curves (10)