SAXSdb — 1d9y

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

PROTEIN (PERIPLASMIC IRON-BINDING PROTEIN)

OrganismNot specified

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 23–331	Not recorded	FE FE (III) ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 10；290 K；PEG 4K CAPS NASCN, pH 10, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.20 Å R-free 0.377

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 1D9Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1O7T Metal nanoclusters bound to the Ferric Binding Protein from Neisseria gonorrhoeae. Deposited 2002-11-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–331（309 aa）	Not recorded	HF5 HF OXO CLUSTER HF5 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；4MG/ML PROTEIN IN 4MM PHOSPHATE, 25MM NAHCO3 PLUS 20% PEG 4000, 0.2M KCL, 0.4M IMIDAZOLE/MALATE BUFFER PH7.7, pH 7.40	Resolution 1.65 Å R-free 0.262
1O7T Metal nanoclusters bound to the Ferric Binding Protein from Neisseria gonorrhoeae. Deposited 2002-11-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 23–331（309 aa）	Not recorded	HF5 HF OXO CLUSTER HF5 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；4MG/ML PROTEIN IN 4MM PHOSPHATE, 25MM NAHCO3 PLUS 20% PEG 4000, 0.2M KCL, 0.4M IMIDAZOLE/MALATE BUFFER PH7.7, pH 7.40	Resolution 1.65 Å R-free 0.262
1O7T Metal nanoclusters bound to the Ferric Binding Protein from Neisseria gonorrhoeae. Deposited 2002-11-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 23–331（309 aa）	Not recorded	HF5 HF OXO CLUSTER HF5 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；4MG/ML PROTEIN IN 4MM PHOSPHATE, 25MM NAHCO3 PLUS 20% PEG 4000, 0.2M KCL, 0.4M IMIDAZOLE/MALATE BUFFER PH7.7, pH 7.40	Resolution 1.65 Å R-free 0.262
1O7T Metal nanoclusters bound to the Ferric Binding Protein from Neisseria gonorrhoeae. Deposited 2002-11-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 23–331（309 aa）	Not recorded	HF3 SMALLEST HF-OXO-PHOSPHATE CLUSTER HF3 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；4MG/ML PROTEIN IN 4MM PHOSPHATE, 25MM NAHCO3 PLUS 20% PEG 4000, 0.2M KCL, 0.4M IMIDAZOLE/MALATE BUFFER PH7.7, pH 7.40	Resolution 1.65 Å R-free 0.262
1O7T Metal nanoclusters bound to the Ferric Binding Protein from Neisseria gonorrhoeae. Deposited 2002-11-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 23–331（309 aa）	Not recorded	HF5 HF OXO CLUSTER HF5 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；4MG/ML PROTEIN IN 4MM PHOSPHATE, 25MM NAHCO3 PLUS 20% PEG 4000, 0.2M KCL, 0.4M IMIDAZOLE/MALATE BUFFER PH7.7, pH 7.40	Resolution 1.65 Å R-free 0.262
1O7T Metal nanoclusters bound to the Ferric Binding Protein from Neisseria gonorrhoeae. Deposited 2002-11-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 23–331（309 aa）	Not recorded	HF5 HF OXO CLUSTER HF5 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；4MG/ML PROTEIN IN 4MM PHOSPHATE, 25MM NAHCO3 PLUS 20% PEG 4000, 0.2M KCL, 0.4M IMIDAZOLE/MALATE BUFFER PH7.7, pH 7.40	Resolution 1.65 Å R-free 0.262
1O7T Metal nanoclusters bound to the Ferric Binding Protein from Neisseria gonorrhoeae. Deposited 2002-11-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 23–331（309 aa）	Not recorded	PHF HF-OXO-PHOSPHATE CLUSTER PHF × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；4MG/ML PROTEIN IN 4MM PHOSPHATE, 25MM NAHCO3 PLUS 20% PEG 4000, 0.2M KCL, 0.4M IMIDAZOLE/MALATE BUFFER PH7.7, pH 7.40	Resolution 1.65 Å R-free 0.262
1O7T Metal nanoclusters bound to the Ferric Binding Protein from Neisseria gonorrhoeae. Deposited 2002-11-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 23–331（309 aa）	Not recorded	PHF HF-OXO-PHOSPHATE CLUSTER PHF × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；4MG/ML PROTEIN IN 4MM PHOSPHATE, 25MM NAHCO3 PLUS 20% PEG 4000, 0.2M KCL, 0.4M IMIDAZOLE/MALATE BUFFER PH7.7, pH 7.40	Resolution 1.65 Å R-free 0.262
1O7T Metal nanoclusters bound to the Ferric Binding Protein from Neisseria gonorrhoeae. Deposited 2002-11-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 23–331（309 aa）	Not recorded	PHF HF-OXO-PHOSPHATE CLUSTER PHF × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；4MG/ML PROTEIN IN 4MM PHOSPHATE, 25MM NAHCO3 PLUS 20% PEG 4000, 0.2M KCL, 0.4M IMIDAZOLE/MALATE BUFFER PH7.7, pH 7.40	Resolution 1.65 Å R-free 0.262
3TYH Crystal structure of oxo-cupper clusters binding to ferric binding protein from Neisseria gonorrhoeae Deposited 2011-09-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–331（309 aa）	Not recorded	CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.8；290 K；0.2M Sodium chloride, 20% PEG 4000, pH 7.8, VAPOR DIFFUSION, temperature 290K	Resolution 2.10 Å R-free 0.169
3TYH Crystal structure of oxo-cupper clusters binding to ferric binding protein from Neisseria gonorrhoeae Deposited 2011-09-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 23–331（309 aa）	Not recorded	CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.8；290 K；0.2M Sodium chloride, 20% PEG 4000, pH 7.8, VAPOR DIFFUSION, temperature 290K	Resolution 2.10 Å R-free 0.169
3TYH Crystal structure of oxo-cupper clusters binding to ferric binding protein from Neisseria gonorrhoeae Deposited 2011-09-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 23–331（309 aa）	Not recorded	CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.8；290 K；0.2M Sodium chloride, 20% PEG 4000, pH 7.8, VAPOR DIFFUSION, temperature 290K	Resolution 2.10 Å R-free 0.169
3TYH Crystal structure of oxo-cupper clusters binding to ferric binding protein from Neisseria gonorrhoeae Deposited 2011-09-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 23–331（309 aa）	Not recorded	CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.8；290 K；0.2M Sodium chloride, 20% PEG 4000, pH 7.8, VAPOR DIFFUSION, temperature 290K	Resolution 2.10 Å R-free 0.169
3TYH Crystal structure of oxo-cupper clusters binding to ferric binding protein from Neisseria gonorrhoeae Deposited 2011-09-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 23–331（309 aa）	Not recorded	CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.8；290 K；0.2M Sodium chloride, 20% PEG 4000, pH 7.8, VAPOR DIFFUSION, temperature 290K	Resolution 2.10 Å R-free 0.169
3TYH Crystal structure of oxo-cupper clusters binding to ferric binding protein from Neisseria gonorrhoeae Deposited 2011-09-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 23–331（309 aa）	Not recorded	CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.8；290 K；0.2M Sodium chloride, 20% PEG 4000, pH 7.8, VAPOR DIFFUSION, temperature 290K	Resolution 2.10 Å R-free 0.169
3TYH Crystal structure of oxo-cupper clusters binding to ferric binding protein from Neisseria gonorrhoeae Deposited 2011-09-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 23–331（309 aa）	Not recorded	CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.8；290 K；0.2M Sodium chloride, 20% PEG 4000, pH 7.8, VAPOR DIFFUSION, temperature 290K	Resolution 2.10 Å R-free 0.169
3TYH Crystal structure of oxo-cupper clusters binding to ferric binding protein from Neisseria gonorrhoeae Deposited 2011-09-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 23–331（309 aa）	Not recorded	CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.8；290 K；0.2M Sodium chloride, 20% PEG 4000, pH 7.8, VAPOR DIFFUSION, temperature 290K	Resolution 2.10 Å R-free 0.169
3TYH Crystal structure of oxo-cupper clusters binding to ferric binding protein from Neisseria gonorrhoeae Deposited 2011-09-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 23–331（309 aa）	Not recorded	CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.8；290 K；0.2M Sodium chloride, 20% PEG 4000, pH 7.8, VAPOR DIFFUSION, temperature 290K	Resolution 2.10 Å R-free 0.169

2 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q50964_NEIGO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–309； UniProt 23–331

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	1d9y
Deposition date deposition_date	1999-10-30
Structure title title	NEISSERIA GONORRHOEAE FERRIC BINDING PROTEIN
Keywords keywords	FERRIC BINDING PROTEIN, PERIPLASMIC BINDING PROTEIN, FBPA, GHONNORHEA, NEISSERIA, METAL BINDING PROTEIN; METAL BINDING 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	20.20 Å
Radius of gyration Rg (electron density) rg_electron	19.18 Å
Forward intensity I(0) i0	19427400.00
Molecular weight molecular_weight	33817.0 kDa
Excluded volume excluded_volume	42548 Å³
Envelope volume envelope_volume	48288 Å³
Hydration-shell volume shell_volume	20865 Å³
Envelope diameter envelope_diameter	63.4 Å
Shell Rg shell_rg	25.68 Å
Envelope Rg envelope_rg	19.34 Å
Shape Rg shape_rg	19.17 Å
Total Rg total_rg	20.11 Å
Total atoms total_atoms	2384
Residues n_residues	309
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	63.6 Å
Rg (real space) rg_real	20.12 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	1.9430e+07
I(0) uncertainty (real space) i0_real_error	2.2160e+05
Rg (reciprocal space) rg_reciprocal	20.13 Å
I(0) (reciprocal space) i0_reciprocal	19430000.0000
Solution quality estimate total_estimate	0.7542
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.6 Å
Skewness Skewness skewness	0.237
Kurtosis Kurtosis kurtosis	-0.429
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5623000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 0.406; Positv: 1.000; Valcen: 0.995; Smooth: 0.897

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PROTEIN (PERIPLASMIC IRON-BINDING PROTEIN)
Molecular weight formula_weight	33704.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2756

DITVYNGQHKEAAQAVADAFTRATGIKVKLNCAKGDQLAGQIKEEGSRSPADVFYSEQIPALATLSAANLLEPLPASTINETRGKGVPVAAKKDWVALSGRSRVVVYDTRKLSEKDLEKSVLNYATPKWKNRIGYVPTSGAFLEQIVAIVKLKGEAAALKWLKGLKEYGKPYAKNSVALQAVENGEIDAALINNYYWHAFAREKGVQNVHTRLNFVRHRDPGALVTYSGAAVLKSSQNKDEAKKFVAFLAGKEGQRALTAVRAEYPLNPHVVSTFNLEPIAKLEAPQVSATTVSEKEHATRLLEQAGMK

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	335

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1d9ya_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

CATH v4.4 (2 domains)

Domain ID domain_id	1d9yA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	1d9yA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

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8. Citations (1)

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Unit-cell length a length_a	40.583 Å
Unit-cell length b length_b	111.009 Å
Unit-cell length c length_c	140.423 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1850
R_work r_work	0.2310
R_free r_free	0.3770

fit	/app/data/saxs_computation/d9/1d9y/1d9y.fit
pddf	/app/data/pr_computation/d9/1d9y/1d9y.pr.out
profile	/app/data/saxs_computation/d9/1d9y/1d9y.dat

NEISSERIA GONORRHOEAE FERRIC BINDING PROTEIN

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

PROTEIN (PERIPLASMIC IRON-BINDING PROTEIN)

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