1nye

Crystal structure of OsmC from E. coli

Method: X-RAY DIFFRACTION

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

Osmotically inducible protein C

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 6	water × 6	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 6	water × 6	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 6	water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OSMC_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–162； UniProt 0–142 Author chain B； PDBConstruct 20–162； UniProt 0–142 Author chain C； PDBConstruct 20–162； UniProt 0–142 Author chain D； PDBConstruct 20–162； UniProt 0–142 Author chain E； PDBConstruct 20–162； UniProt 0–142 Author chain F； PDBConstruct 20–162； UniProt 0–142

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	1nye
Deposition date deposition_date	2003-02-12
Structure title title	Crystal structure of OsmC from E. coli
Keywords keywords	;OsmC, Structural genomics, peroxiredoxin, BSGC structure funded by NIH, Protein Structure Initiative, PSI, Berkeley Structural Genomics Center, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

1nye__assembly_6__model_1

Assembly 6 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1nye__assembly_6__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1nye__assembly_6__model_1 | P(r) · Pending

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

Rg（Guinier）	39.81 Å
Rg (electron density)	40.56 Å
Total Rg	40.54 Å
Atom count	6813
Residues	910
Excluded volume	121120 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1nye__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1nye__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1nye__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1nye__assembly_4__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1nye__assembly_5__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1nye__assembly_6__model_1`	hexameric （6）	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 (2)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1nyea_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.227 — OsmC-like
Superfamily Superfamily superfamily	d.227.1 — OsmC-like
Family Family family	d.227.1.1 — Ohr/OsmC resistance proteins

Domain ID domain_id	d1nyeb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.227 — OsmC-like
Superfamily Superfamily superfamily	d.227.1 — OsmC-like
Family Family family	d.227.1.1 — Ohr/OsmC resistance proteins

Domain ID domain_id	d1nyec1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.227 — OsmC-like
Superfamily Superfamily superfamily	d.227.1 — OsmC-like
Family Family family	d.227.1.1 — Ohr/OsmC resistance proteins

Domain ID domain_id	d1nyec2
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	d1nyed1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.227 — OsmC-like
Superfamily Superfamily superfamily	d.227.1 — OsmC-like
Family Family family	d.227.1.1 — Ohr/OsmC resistance proteins

Domain ID domain_id	d1nyed2
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	d1nyee1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.227 — OsmC-like
Superfamily Superfamily superfamily	d.227.1 — OsmC-like
Family Family family	d.227.1.1 — Ohr/OsmC resistance proteins

Domain ID domain_id	d1nyee2
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	d1nyef1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.227 — OsmC-like
Superfamily Superfamily superfamily	d.227.1 — OsmC-like
Family Family family	d.227.1.1 — Ohr/OsmC resistance proteins

Domain ID domain_id	d1nyef2
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	1nyeA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	20 — K homology (KH) domain

Domain ID domain_id	1nyeB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	20 — K homology (KH) domain

Domain ID domain_id	1nyeC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	20 — K homology (KH) domain

Domain ID domain_id	1nyeD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	20 — K homology (KH) domain

Domain ID domain_id	1nyeE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	20 — K homology (KH) domain

Domain ID domain_id	1nyeF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	20 — K homology (KH) domain

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Unit-cell length a length_a	49.529 Å
Unit-cell length b length_b	90.291 Å
Unit-cell length c length_c	112.677 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	19.960 Å
R factor r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.2770

Description description	Osmotically inducible protein C
Molecular weight formula_weight	17453.6 kDa
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	6900

Crystal structure of OsmC from E. coli

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

Osmotically inducible protein C

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

1nye__assembly_6__model_1

1nye__assembly_6__model_1 | I(q)

1nye__assembly_6__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (10 domains)

CATH v4.4 (6 domains)

7. Citations (1)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	87

Crystal structure of OsmC from E. coli

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

Osmotically inducible protein C

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

1nye__assembly_6__model_1

1nye__assembly_6__model_1 | I(q)

1nye__assembly_6__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (10 domains)

CATH v4.4 (6 domains)

7. Citations (1)