2r7a

Crystal Structure of a Periplasmic Heme Binding Protein from Shigella dysenteriae

Method: X-RAY DIFFRACTION

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

Bacterial heme binding protein

Shigella dysenteriae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PROTOPORPHYRIN IX CONTAINING FE × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O70018_SHIDY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–256； UniProt 49–304 Author chain B； PDBConstruct 1–256； UniProt 49–304 Author chain C； PDBConstruct 1–256； UniProt 49–304 Author chain D； PDBConstruct 1–256； UniProt 49–304

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	2r7a
Deposition date deposition_date	2007-09-07
Structure title title	Crystal Structure of a Periplasmic Heme Binding Protein from Shigella dysenteriae
Keywords keywords	periplasmic binding protein, heme transport, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

2r7a__assembly_2__model_1

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

Download this curve (.dat)

2r7a__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2r7a__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.72 Å
Rg (electron density)	24.59 Å
Total Rg	25.49 Å
Atom count	3873
Residues	511
Excluded volume	69186 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2r7a__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2r7a__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Bacterial heme binding protein
Molecular weight formula_weight	27582.5 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	8283

AAERIVVAGGSLTELIYAMGAGERVVGVDETTSYPPETAKLPHIGYWKQLSSEGILSLRPDSVITWQDAGPQIVLDQLRAQKVNVVTLPRVPATLEQMYANIRQLAKTLQVPEQGDALVTQINQRLERVQQNVAAKKAPVKAMFILSAGGSAPQVAGKGSVADAILSLAGAENVATHQQYKSYSAESLIAANPEVIVVTSQMVDGDINRLRSIAGITHTAAWKNQRIITVDQNLILGMGPRIADVVESLHQQLWPQ

Source Source

Source organism organism	Shigella dysenteriae
NCBI taxonomy ID ncbi_taxonomy_id	622
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 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	499

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2r7aa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.92 — Chelatase-like
Superfamily Superfamily superfamily	c.92.2 — 'Helical backbone' metal receptor
Family Family family	c.92.2.0 — automated matches

Domain ID domain_id	d2r7ab_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.92 — Chelatase-like
Superfamily Superfamily superfamily	c.92.2 — 'Helical backbone' metal receptor
Family Family family	c.92.2.0 — automated matches

Domain ID domain_id	d2r7ac_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.92 — Chelatase-like
Superfamily Superfamily superfamily	c.92.2 — 'Helical backbone' metal receptor
Family Family family	c.92.2.0 — automated matches

Domain ID domain_id	d2r7ad_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.92 — Chelatase-like
Superfamily Superfamily superfamily	c.92.2 — 'Helical backbone' metal receptor
Family Family family	c.92.2.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	2r7aA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	2r7aA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	2r7aB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	2r7aB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	2r7aC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	2r7aC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	2r7aD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	2r7aD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

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Unit-cell length a length_a	54.700 Å
Unit-cell length b length_b	73.308 Å
Unit-cell length c length_c	73.316 Å
Unit-cell angle α angle_alpha	70.25 °
Unit-cell angle β angle_beta	79.02 °
Unit-cell angle γ angle_gamma	90.22 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	43.860 Å
R factor r_factor	0.2100
R_work r_work	0.2100
R_free r_free	0.2550

Crystal Structure of a Periplasmic Heme Binding Protein from Shigella dysenteriae

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

Bacterial heme binding protein

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

2r7a__assembly_2__model_1

2r7a__assembly_2__model_1 | I(q)

2r7a__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 (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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of a Periplasmic Heme Binding Protein from Shigella dysenteriae

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

Bacterial heme binding 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2r7a__assembly_2__model_1

2r7a__assembly_2__model_1 | I(q)

2r7a__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 (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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)