SAXSdb — 3ak5

▼

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

Hemoglobin-binding protease hbp

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HBP_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–481； UniProt 53–533 Author chain A； PDBConstruct 483–975； UniProt 608–1100 Author chain B； PDBConstruct 1–481； UniProt 53–533 Author chain B； PDBConstruct 483–975； UniProt 608–1100 Author chain C； PDBConstruct 1–481； UniProt 53–533 Author chain C； PDBConstruct 483–975； UniProt 608–1100 Author chain D； PDBConstruct 1–481； UniProt 53–533 Author chain D； PDBConstruct 483–975； UniProt 608–1100

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3ak5
Deposition date deposition_date	2010-07-07
Structure title title	Hemoglobin protease (Hbp) passenger missing domain-2
Keywords keywords	autotransporter, beta helix, mutant, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3ak5__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3ak5__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ak5__assembly_4__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	39.28 Å
Rg (electron density)	39.75 Å
Total Rg	39.92 Å
Atom count	7114
Residues	948
Excluded volume	124490 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ak5__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ak5__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3ak5__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3ak5__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Hemoglobin-binding protease hbp
Molecular weight formula_weight	103724.6 kDa
EC 编号 ec_number	3.4.21.-
Mutation mutation	PROTEASE DELETION MUTANT
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	30307

GTVNNELGYQLFRDFAENKGMFRPGATNIAIYNKQGEFVGTLDKAAMPDFSAVDSEIGVATLINPQYIASVKHNGGYTNVSFGDGENRYNIVDRNNAPSLDFHAPRLDKLVTEVAPTAVTAQGAVAGAYLDKERYPVFYRLGSGTQYIKDSNGQLTKMGGAYSWLTGGTVGSLSSYQNGEMISTSSGLVFDYKLNGAMPIYGEAGDSGSPLFAFDTVQNKWVLVGVLTAGNGAGGRGNNWAVIPLDFIGQKFNEDNDAPVTFRTSEGGALEWSFNSSTGAGALTQGTTTYAMHGQQGNDLNAGKNLIFQGQNGQINLKDSVSQGAGSLTFRDNYTVTTSNGSTWTGAGIVVDNGVSVNWQVNGVKGDNLHKIGEGTLTVQGTGINEGGLKVGDGKVVLNQQADNKGQVQAFSSVNIASGRPTVVLTDERQVNPDTVSWGYRGGTLDVNGNSLTFHQLKAADYGAVLANNVDKRATITLDYAGNTAGYLFHGQLKGNLNVDNRLPEGVTGALVMDGAADISGTFTQENGRLTLQGHPVIHAYNTQSVADKLAASGDHSVLTQPTSFSQEDWENRSFTFDRLSLKNTDFGLGRNATLNTTIQADNSSVTLGDSRVFIDKNDGQGTAFTLEEGTSVATKDADKSVFNGTVNLDNQSVLNINDIFNGGIQANNSTVNISSDSAVLGNSTLTSTALNLNKGANALASQSFVSDGPVNISDATLSLNSRPDEVSHTLLPVYDYAGSWNLKGDDARLNVGPYSMLSGNINVQDKGTVTLGGEGELSPDLTLQNQMLYSLFNGYRNIWSGSLNAPDATVSMTDTQWSMNGNSTAGNMKLNRTIVGFNGGTSPFTTLTTDNLDAVQSAFVMRTDLNKADKLVINKSATGHDNSIWVNFLKKPSNKDTLDIPLVSAPEATADNLFRASTRVVGFSDVTPILSVRKEDGKKEWVLDGYQVARNDGQGKAAATFMHISYNNFITEVN

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1485

▼

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3ak5A01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	3ak5A02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3ak5B01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	3ak5B02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3ak5C01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	3ak5C02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3ak5D01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	3ak5D02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily	20 —

▶

Unit-cell length a length_a	292.803 Å
Unit-cell length b length_b	53.936 Å
Unit-cell length c length_c	335.953 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.32 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	48.560 Å
R factor r_factor	0.2255
R_work r_work	0.2255
R_free r_free	0.2801

Hemoglobin protease (Hbp) passenger missing domain-2

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

Hemoglobin-binding protease hbp

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3ak5__assembly_4__model_1

3ak5__assembly_4__model_1 | I(q)

3ak5__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Hemoglobin protease (Hbp) passenger missing domain-2

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

Hemoglobin-binding protease hbp

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3ak5__assembly_4__model_1

3ak5__assembly_4__model_1 | I(q)

3ak5__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)