SAXSdb — 1d9v

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

PROTEIN (iron-utilization periplasmic protein)

Haemophilus influenzae

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 24–332	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；PEG 1450, HEPES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 17K	Resolution 1.75 Å R-free 0.263

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 1D9V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1MRP FERRIC-BINDING PROTEIN FROM HAEMOPHILUS INFLUENZAE Deposited 1997-05-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 24–332（309 aa）	Not recorded	FE FE (III) ION × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.6；20% PEG 4000, 400 MM IMIDAZOLE/MALATE PH 6.6, 200 MM NACL	Resolution 1.60 Å R-free 0.240
1NNF Crystal Structure Analysis of Haemophlius Influenzae Ferric-ion Binding Protein H9Q Mutant Form Deposited 2003-01-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–332（309 aa）	Mutation：H9Q	FE FE (III) ION × 1 EDT {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；PEG 5000, Tris HCl, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.10 Å R-free 0.180
1QVS Crystal Structure of Haemophilus influenzae H9A mutant Holo Ferric ion-Binding Protein A Deposited 2003-08-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–332（309 aa）	Mutation：H9A	FE FE (III) ION × 3 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；PEG 550 MME, Tris, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.226
1QW0 Crystal Structure of Haemophilus influenzae N175L mutant Holo Ferric ion-Binding Protein A Deposited 2003-08-29	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–332（309 aa）	Mutation：N175L	FE FE (III) ION × 4 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；277 K；PEG 550 MME, Tris, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.271
2O68 Crystal Structure of Haemophilus influenzae Q58L mutant FbpA Deposited 2006-12-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–332（309 aa）	Mutation：Q58L	FE FE (III) ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 550 MME, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 1.70 Å R-free 0.248
2O69 Crystal Structure of Haemophilus influenzae N193L mutant FbpA Deposited 2006-12-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–332（309 aa）	Mutation：N193L	FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 550 MME, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.00 Å R-free 0.259
2O6A Crystal structure of the Haemophilus influenzae E57A mutant FbpA Deposited 2006-12-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–332（309 aa）	Mutation：E57A	FE FE (III) ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；277 K；PEG 550 MME, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K, pH 8.50	Resolution 1.80 Å R-free 0.250
3KN7 Crystal Structure of Haemophilus influenzae Y195A mutant Holo Ferric ion-Binding Protein A Deposited 2009-11-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–332（309 aa）	Mutation：Y195A	FE FE (III) ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；34% PEG 550 MME, 0.1 M Tris pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.71 Å R-free 0.237
3KN8 Crystal Structure of Haemophilus influenzae Y196A mutant Holo Ferric ion-Binding Protein A Deposited 2009-11-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–332（309 aa）	Mutation：Y196A	FE FE (III) ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；28% PEG 550 MME, 0.1M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.89 Å R-free 0.235
3OD7 Haemophilus influenzae ferric binding protein A -Iron Loaded Deposited 2010-08-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–332（309 aa）	Not recorded	FE FE (III) ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；303 K；18% PEG 4000, 0.4M Imidazole/Malate, 0.2M NaCl, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 303K	Resolution 1.80 Å R-free 0.250
3ODB Haemophilus influenzae ferric binding protein A -Iron Loaded -open Conformation Deposited 2010-08-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–332（309 aa）	Not recorded	FE FE (III) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；25% PEG 1000, 0.1 M MES, pH 6.5 , VAPOR DIFFUSION, temperature 293K	Resolution 1.62 Å R-free 0.252

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FBPA_HAEIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–309； UniProt 24–332

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	1d9v
Deposition date deposition_date	1999-10-30
Structure title title	HAEMOPHILUS INFLUENZAE FERRIC-BINDING PROTEIN APO FORM
Keywords keywords	FERRIC, BINDING PROTEIN, IRON, APO FORM, PERIPLASMIC PROTEIN, ABC CASSETTE RECEPTOR PROTEIN, 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	20.81 Å
Radius of gyration Rg (electron density) rg_electron	19.94 Å
Forward intensity I(0) i0	19032100.00
Molecular weight molecular_weight	33821.0 kDa
Excluded volume excluded_volume	42670 Å³
Envelope volume envelope_volume	49414 Å³
Hydration-shell volume shell_volume	20817 Å³
Envelope diameter envelope_diameter	67.4 Å
Shell Rg shell_rg	26.13 Å
Envelope Rg envelope_rg	19.98 Å
Shape Rg shape_rg	19.91 Å
Total Rg total_rg	20.89 Å
Total atoms total_atoms	2387
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	64.9 Å
Rg (real space) rg_real	20.75 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	1.9030e+07
I(0) uncertainty (real space) i0_real_error	2.5260e+05
Rg (reciprocal space) rg_reciprocal	20.77 Å
I(0) (reciprocal space) i0_reciprocal	19030000.0000
Solution quality estimate total_estimate	0.8255
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.277
Kurtosis Kurtosis kurtosis	-0.427
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6013000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 0.998; 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)

Entity 1 Entity 1 polymer

Description description	PROTEIN (iron-utilization periplasmic protein)
Molecular weight formula_weight	33769.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2550

DITVYNGQHKEAATAVAKAFEQETGIKVTLNSGKSEQLAGQLKEEGDKTPADVFYTEQTATFADLSEAGLLAPISEQTIQQTAQKGVPLAPKKDWIALSGRSRVVVYDHTKLSEKDMEKSVLDYATPKWKGKIGYVSTSGAFLEQVVALSKMKGDKVALNWLKGLKENGKLYAKNSVALQAVENGEVPAALINNYYWYNLAKEKGVENLKSRLYFVRHQDPGALVSYSGAAVLKASKNQAEAQKFVDFLASKKGQEALVAARAEYPLRADVVSPFNLEPYEKLEAPVVSATTAQDKEHAIKLIEEAGLK

来源 Source

来源生物 organism	Haemophilus influenzae
NCBI Class编号 ncbi_taxonomy_id	727
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	153

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1d9va_
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	1d9vA01
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	1d9vA02
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	106.746 Å
Unit-cell length b length_b	77.418 Å
Unit-cell length c length_c	34.221 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	100.000 Å
R factor r_factor	—
R_work r_work	0.1790
R_free r_free	0.2630

fit	/app/data/saxs_computation/d9/1d9v/1d9v.fit
pddf	/app/data/pr_computation/d9/1d9v/1d9v.pr.out
profile	/app/data/saxs_computation/d9/1d9v/1d9v.dat

HAEMOPHILUS INFLUENZAE FERRIC-BINDING PROTEIN APO FORM

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

PROTEIN (iron-utilization periplasmic 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