SAXSdb — 3ddr

▼

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

HasR protein

Serratia marcescens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Hemophore HasA × 1 （Q54450） SODIUM ION × 1 GLYCEROL × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Hemophore HasA × 1 （Q54450） SODIUM ION × 1 GLYCEROL × 5 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q79AD2_SERMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 14–865； UniProt 48–899 Author chain B； PDBConstruct 14–865； UniProt 48–899

Hemophore HasA

Serratia marcescens

UniProt Q54450

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	HasR protein × 1 （Q79AD2） SODIUM ION × 1 GLYCEROL × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	HasR protein × 1 （Q79AD2） SODIUM ION × 1 GLYCEROL × 5 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HASA_SERMA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 20–206； UniProt 2–188 Author chain D； PDBConstruct 20–206； UniProt 2–188

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	3ddr
Deposition date deposition_date	2008-06-06
Structure title title	Structure of the Serratia marcescens hemophore receptor HasR-Ile671Gly mutant in complex with its hemophore HasA and heme
Keywords keywords	;outer membrane protein, beta-barrel, hemophore receptor, Membrane, Outer membrane, TonB box, Heme, Iron, Metal-binding, Secreted, MEMBRANE PROTEIN-HEME BINDING PROTEIN COMPLEX ;; MEMBRANE PROTEIN/HEME BINDING PROTEIN
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.

3ddr__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3ddr__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ddr__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	31.13 Å
Rg (electron density)	31.03 Å
Total Rg	31.47 Å
Atom count	7135
Residues	915
Excluded volume	124580 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ddr__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ddr__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	HasR protein
Molecular weight formula_weight	94898.6 kDa
Mutation mutation	I671G
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	14259

AQAEASSAQAAQQKNFNIAAQPLQSAMLRFAEQAGMQVFFDEVKLDGMQAAALNGSMSVEQGLRRLIGGNPVAFRLQPQGQIVLSRLPTANGDGGALALDSLTVLGAGGNNANDWVYDEPRSVSVISREQMDNRPARHAADILEQTTGAYSSVSQQDPALSVNIRGIQDYGRVNMNIDGMRQNFQKSGHGQRNGTMYIDSELLSGVTIDKGTTGGMGSAGTLGGIATFNTVSASDFLAPGKELGGKLHASTGDNGTHFIGSGILALGNETGDILLAASERHLGDYWPGNKGDIGNIRINNDTGNYDRYAESIKNNKIPDTHYRMHSRLAKVGWNLPANQRLQLSYLQTQTASPIAGTLTNLGTRPPYELGWKRTGYTDVMARNAAFDYSLAPEDVDWLDFQAKLYYVDTQDDSDTYSTSSLLDNGYATRTRLRTYGAQAQNTSRFSLAPGHDFRANYGLEFYYDKATSDSSRQGMEGVTPAGNRSVASLFANLTYDYDGWLTLEGGLRYDRYRLRGQTGLSYPDLAKDGQRYTIDNPCKALRLTGCSTTTREDWDVDRDQGKLSPTLAVAVRPGVEWLELYTTYGKSWRPPAITETLTNGSAHSSSTQYPNPFLQPERSRAWEVGFNVQQPDLWFEGDRLVAKVAYFDTKVDNYINLAIDRNKPGLVQPSGGNAAYVNNLSKTRFRGLEYQLNYDAGVFYADLTYTHMIGKNEFCSNKAWLGGRLRYGDGSRRGNFYVEPDAASNDFVTCDGGTQFGSAAYLPGDRGSVTLGGRAFDRKLDAGVTVRFAPGYQDSSVPSNYPYLADWPKYTLFDLYASYKLTDSLTLRGSVENLTNRAYVVSYGETLANTLGRGRTVQGGVEYRF

Source Source

Source organism organism	Serratia marcescens
NCBI taxonomy ID ncbi_taxonomy_id	615
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Hemophore HasA
Molecular weight formula_weight	21523.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MRGSHHHHHHGIRMRARYPAFSVNYDSSFGGYSIHDYLGQWASTFGDVNHTNGNVTDANSGGFYGGSLSGSQYAISSTANQVTAFVAGGNLTYTLFNEPAHTLYGQLDSLSFGDGLSGGDTSPYSIQVPDVSFGGLNLSSLQAQGHDGVVHQVVYGLMSGDTGALETALNGILDDYGLSVNSTFDQVAAATAVGVQHADSPELLAA

Source Source

Source organism organism	Serratia marcescens
NCBI taxonomy ID ncbi_taxonomy_id	615
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

▼

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3ddrc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.35 — Heme-binding protein A (HasA)
Superfamily Superfamily superfamily	d.35.1 — Heme-binding protein A (HasA)
Family Family family	d.35.1.1 — Heme-binding protein A (HasA)

Domain ID domain_id	d3ddrc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3ddrd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.35 — Heme-binding protein A (HasA)
Superfamily Superfamily superfamily	d.35.1 — Heme-binding protein A (HasA)
Family Family family	d.35.1.1 — Heme-binding protein A (HasA)

Domain ID domain_id	d3ddrd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	3ddrA01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	130 — Ferric Hydroxamate Uptake Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — TonB-dependent receptor, plug domain

Domain ID domain_id	3ddrA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	170 — Maltoporin; Chain A
Homologous superfamily homologous superfamily	20 — TonB-dependent receptor, beta-barrel domain

Domain ID domain_id	3ddrB01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	130 — Ferric Hydroxamate Uptake Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — TonB-dependent receptor, plug domain

Domain ID domain_id	3ddrB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	170 — Maltoporin; Chain A
Homologous superfamily homologous superfamily	20 — TonB-dependent receptor, beta-barrel domain

Domain ID domain_id	3ddrC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1500 — Heme-binding Protein A; Chain: A;
Homologous superfamily homologous superfamily	10 — Haem-binding HasA

Domain ID domain_id	3ddrD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1500 — Heme-binding Protein A; Chain: A;
Homologous superfamily homologous superfamily	10 — Haem-binding HasA

▶

Unit-cell length a length_a	157.410 Å
Unit-cell length b length_b	162.720 Å
Unit-cell length c length_c	597.010 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	F 2 2 2
Space-group number int_tables_number	22
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	39.250 Å
R factor r_factor	0.2270
R_work r_work	0.2260
R_free r_free	0.2620

Structure of the Serratia marcescens hemophore receptor HasR-Ile671Gly mutant in complex with its hemophore HasA and heme

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

HasR protein

State in the Current Structure

Other States of the Same Protein in the Database

Hemophore HasA

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

3ddr__assembly_2__model_1

3ddr__assembly_2__model_1 | I(q)

3ddr__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structure of the Serratia marcescens hemophore receptor HasR-Ile671Gly mutant in complex with its hemophore HasA and heme

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

HasR protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Hemophore HasA

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

3ddr__assembly_2__model_1

3ddr__assembly_2__model_1 | I(q)

3ddr__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)