SAXSdb — 9ypm

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Mangotoxin biosynthesis protein MboA

Pseudomonas syringae

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 1–225	Not recorded	SO4 SULFATE ION × 4 CL CHLORIDE ION × 4 FE2 FE (II) ION × 2 GOL GLYCEROL × 12	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method in an Coy anaerobic chamber with an atmosphere of < 5 ppm of O2. Hanging drops were prepared by combining equal volumes of MboA (9 mg/mL) protein solution, reservoir solution (0.6 M lithium sulfate and 0.1 M sodium acetate, pH 4.6), and 0.2 uL of a 1:1000 dilution microseed master stock generated from apo crystals for a total drop volume of 2.2 uL. The Fe(II) + substrate bound structure was prepared by incubating apo crystals with 0.4 uL of 100 mM LAR peptide and 100 mM Fe2+ in 0.1 M sodium acetate, pH 4.6 for two hours prior to looping. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	Resolution 2.45 Å R-free 0.195
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–225	Not recorded	SO4 SULFATE ION × 5 CL CHLORIDE ION × 4 FE2 FE (II) ION × 2 GOL GLYCEROL × 7 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method in an Coy anaerobic chamber with an atmosphere of < 5 ppm of O2. Hanging drops were prepared by combining equal volumes of MboA (9 mg/mL) protein solution, reservoir solution (0.6 M lithium sulfate and 0.1 M sodium acetate, pH 4.6), and 0.2 uL of a 1:1000 dilution microseed master stock generated from apo crystals for a total drop volume of 2.2 uL. The Fe(II) + substrate bound structure was prepared by incubating apo crystals with 0.4 uL of 100 mM LAR peptide and 100 mM Fe2+ in 0.1 M sodium acetate, pH 4.6 for two hours prior to looping. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	Resolution 2.45 Å R-free 0.195
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–225	Not recorded	SO4 SULFATE ION × 3 CL CHLORIDE ION × 2 FE2 FE (II) ION × 2 GOL GLYCEROL × 10 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method in an Coy anaerobic chamber with an atmosphere of < 5 ppm of O2. Hanging drops were prepared by combining equal volumes of MboA (9 mg/mL) protein solution, reservoir solution (0.6 M lithium sulfate and 0.1 M sodium acetate, pH 4.6), and 0.2 uL of a 1:1000 dilution microseed master stock generated from apo crystals for a total drop volume of 2.2 uL. The Fe(II) + substrate bound structure was prepared by incubating apo crystals with 0.4 uL of 100 mM LAR peptide and 100 mM Fe2+ in 0.1 M sodium acetate, pH 4.6 for two hours prior to looping. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	Resolution 2.45 Å R-free 0.195
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1–225	Not recorded	SO4 SULFATE ION × 3 CL CHLORIDE ION × 2 FE2 FE (II) ION × 2 GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method in an Coy anaerobic chamber with an atmosphere of < 5 ppm of O2. Hanging drops were prepared by combining equal volumes of MboA (9 mg/mL) protein solution, reservoir solution (0.6 M lithium sulfate and 0.1 M sodium acetate, pH 4.6), and 0.2 uL of a 1:1000 dilution microseed master stock generated from apo crystals for a total drop volume of 2.2 uL. The Fe(II) + substrate bound structure was prepared by incubating apo crystals with 0.4 uL of 100 mM LAR peptide and 100 mM Fe2+ in 0.1 M sodium acetate, pH 4.6 for two hours prior to looping. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	Resolution 2.45 Å R-free 0.195

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 9YPM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9YPI MboA HDO apo structure Deposited 2025-10-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–225（225 aa）	Not recorded	CL CHLORIDE ION × 5 SO4 SULFATE ION × 1 NA SODIUM ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method. Hanging drops were prepared by combining equal volumes of MboA (18 mg per mL) protein solution and reservoir solution (1.2 M lithium sulfate and 0.1 M sodium acetate, pH 4.6) for a total drop volume of 2 uL. Crystals typically grew in about approximately 1 to 2 weeks. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	Resolution 2.49 Å R-free 0.221
9YPI MboA HDO apo structure Deposited 2025-10-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–225（225 aa）	Not recorded	CL CHLORIDE ION × 6 SO4 SULFATE ION × 1 NA SODIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method. Hanging drops were prepared by combining equal volumes of MboA (18 mg per mL) protein solution and reservoir solution (1.2 M lithium sulfate and 0.1 M sodium acetate, pH 4.6) for a total drop volume of 2 uL. Crystals typically grew in about approximately 1 to 2 weeks. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	Resolution 2.49 Å R-free 0.221
9YPI MboA HDO apo structure Deposited 2025-10-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–225（225 aa）	Not recorded	CL CHLORIDE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method. Hanging drops were prepared by combining equal volumes of MboA (18 mg per mL) protein solution and reservoir solution (1.2 M lithium sulfate and 0.1 M sodium acetate, pH 4.6) for a total drop volume of 2 uL. Crystals typically grew in about approximately 1 to 2 weeks. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	Resolution 2.49 Å R-free 0.221
9YPI MboA HDO apo structure Deposited 2025-10-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–225（225 aa）	Not recorded	CL CHLORIDE ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method. Hanging drops were prepared by combining equal volumes of MboA (18 mg per mL) protein solution and reservoir solution (1.2 M lithium sulfate and 0.1 M sodium acetate, pH 4.6) for a total drop volume of 2 uL. Crystals typically grew in about approximately 1 to 2 weeks. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	Resolution 2.49 Å R-free 0.221
9YPL MboA with Leu-Ala-Arg peptide substrate bound Deposited 2025-10-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–225（225 aa）	Not recorded	SO4 SULFATE ION × 2 CL CHLORIDE ION × 5 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method. Hanging drops were prepared by combining equal volumes of MboA (9 mg per mL) protein solution and reservoir solution (0.4 M lithium sulfate and 0.1 M sodium acetate, pH 4.8) for a total drop volume of 2 uL. The substrate bound structure was prepared by incubating apo crystals with 0.3 uL of 100 mM LAR in 0.1 M sodium acetate, pH 4.6 for two hours prior to looping. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	Resolution 2.20 Å R-free 0.194
9YPL MboA with Leu-Ala-Arg peptide substrate bound Deposited 2025-10-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–225（225 aa）	Not recorded	SO4 SULFATE ION × 1 CL CHLORIDE ION × 4 GOL GLYCEROL × 1 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method. Hanging drops were prepared by combining equal volumes of MboA (9 mg per mL) protein solution and reservoir solution (0.4 M lithium sulfate and 0.1 M sodium acetate, pH 4.8) for a total drop volume of 2 uL. The substrate bound structure was prepared by incubating apo crystals with 0.3 uL of 100 mM LAR in 0.1 M sodium acetate, pH 4.6 for two hours prior to looping. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	Resolution 2.20 Å R-free 0.194
9YPL MboA with Leu-Ala-Arg peptide substrate bound Deposited 2025-10-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–225（225 aa）	Not recorded	CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method. Hanging drops were prepared by combining equal volumes of MboA (9 mg per mL) protein solution and reservoir solution (0.4 M lithium sulfate and 0.1 M sodium acetate, pH 4.8) for a total drop volume of 2 uL. The substrate bound structure was prepared by incubating apo crystals with 0.3 uL of 100 mM LAR in 0.1 M sodium acetate, pH 4.6 for two hours prior to looping. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	Resolution 2.20 Å R-free 0.194
9YPL MboA with Leu-Ala-Arg peptide substrate bound Deposited 2025-10-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–225（225 aa）	Not recorded	SO4 SULFATE ION × 3 CL CHLORIDE ION × 2 GOL GLYCEROL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；MboA crystals were prepared via the hanging drop vapor diffusion method. Hanging drops were prepared by combining equal volumes of MboA (9 mg per mL) protein solution and reservoir solution (0.4 M lithium sulfate and 0.1 M sodium acetate, pH 4.8) for a total drop volume of 2 uL. The substrate bound structure was prepared by incubating apo crystals with 0.3 uL of 100 mM LAR in 0.1 M sodium acetate, pH 4.6 for two hours prior to looping. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2	Resolution 2.20 Å R-free 0.194

2 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A244EXR3_PSESX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 26–250； UniProt 1–225 Author chain B； PDBConstruct 26–250； UniProt 1–225 Author chain C； PDBConstruct 26–250； UniProt 1–225 Author chain D； PDBConstruct 26–250； UniProt 1–225

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9ypm
Deposition date deposition_date	2025-10-14
Structure title title	MboA with Leu-Ala-Arg peptide substrate and two Fe(II) ions bound
Keywords keywords	Heme-oxygenase like domain containing enzyme, HDO, Di-iron oxidase, alkynase, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	30.88 Å
Radius of gyration Rg (electron density) rg_electron	29.83 Å
Forward intensity I(0) i0	203549000.00
Molecular weight molecular_weight	111590.0 kDa
Excluded volume excluded_volume	138340 Å³
Envelope volume envelope_volume	166010 Å³
Hydration-shell volume shell_volume	44495 Å³
Envelope diameter envelope_diameter	98.9 Å
Shell Rg shell_rg	38.46 Å
Envelope Rg envelope_rg	29.94 Å
Shape Rg shape_rg	29.83 Å
Total Rg total_rg	30.54 Å
Total atoms total_atoms	7767
Residues n_residues	941
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	93.4 Å
Rg (real space) rg_real	30.70 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	2.0350e+08
I(0) uncertainty (real space) i0_real_error	2.9440e+06
Rg (reciprocal space) rg_reciprocal	30.78 Å
I(0) (reciprocal space) i0_reciprocal	203600000.0000
Solution quality estimate total_estimate	0.9071
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	40.3 Å
Skewness Skewness skewness	0.130
Kurtosis Kurtosis kurtosis	-0.529
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	56500000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.933

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Mangotoxin biosynthesis protein MboA
Molecular weight formula_weight	28433.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8119

MGHHHHHHHHHHSSGHLEVLFQGPHMISTAEMLKTLETTVDTCLEAEFKKDTVMGEFHKGDWFNESYYKRHILECVIRIHMNNELDARAVQVAAIDNISAAKQLSYYLYDEFGHDEMFGQDLITYGYSASDIKAEFAFPETWKLMGYLNFCVSKFGPLSSITWDWFLEYYGDKYSSFITQKASASMGQPAVSGAASHVAFDEAEDHSGMMNNMLSSVIKDEKDLAKAVVHIKAFVPMVGEYFQALRAATL

来源 Source

来源生物 organism	Pseudomonas syringae
NCBI Class编号 ncbi_taxonomy_id	317
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	LEU-ALA-ARG peptide substrate
Molecular weight formula_weight	359.4 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,K,L,M

LAR

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 5 Entity 5 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	36

Entity 7 Entity 7 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	270

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8. Citations (1)

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Unit-cell length a length_a	157.094 Å
Unit-cell length b length_b	157.094 Å
Unit-cell length c length_c	157.423 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	90.760 Å
R factor r_factor	0.1642
R_work r_work	0.1626
R_free r_free	0.1951

fit	/app/data/saxs_computation/yp/9ypm/9ypm.fit
pddf	/app/data/pr_computation/yp/9ypm/9ypm.pr.out
profile	/app/data/saxs_computation/yp/9ypm/9ypm.dat

MboA with Leu-Ala-Arg peptide substrate and two Fe(II) ions bound

1. Protein Identity and Related Structures Protein Identity & Related Structures

Mangotoxin biosynthesis protein MboA

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)