1nmp

Structural genomics, ybgI protein, unknown function

Method: X-RAY DIFFRACTION

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

Hypothetical protein ybgI

Escherichia coli, Escherichia coli O157:H7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	MAGNESIUM ION × 11 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	MAGNESIUM ION × 12 water × 6	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 6	MAGNESIUM ION × 9 water × 6	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 6	MAGNESIUM ION × 12 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YBGI_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–247； UniProt 1–247 Author chain B； PDBConstruct 1–247； UniProt 1–247 Author chain C； PDBConstruct 1–247； UniProt 1–247 Author chain D； PDBConstruct 1–247； UniProt 1–247 Author chain E； PDBConstruct 1–247； UniProt 1–247 Author chain F； PDBConstruct 1–247； UniProt 1–247

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	1nmp
Deposition date deposition_date	2003-01-10
Structure title title	Structural genomics, ybgI protein, unknown function
Keywords keywords	ybgI, hypothetical protein, toroidal structure, Structure 2 Function Project, S2F, Structural Genomics, 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.

1nmp__assembly_4__model_1

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

Download this curve (.dat)

1nmp__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1nmp__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	37.15 Å
Rg (electron density)	36.29 Å
Total Rg	36.99 Å
Atom count	11394
Residues	1482
Excluded volume	201830 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1nmp__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1nmp__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1nmp__assembly_3__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1nmp__assembly_4__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 (3)

Entity 1 Entity 1 polymer

Description description	Hypothetical protein ybgI
Molecular weight formula_weight	26919.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	11969

MKNTELEQLINEKLNSAAISDYAPNGLQVEGKETVQKIVTGVTASQALLDEAVRLGADAVIVHHGYFWKGESPVIRGMKRNRLKTLLANDINLYGWHLPLDAHPELGNNAQLAALLGITVMGEIEPLVPWGELTMPVPGLELASWIEARLGRKPLWCGDTGPEVVQRVAWCTGGGQSFIDSAARFGVDAFITGEVSEQTIHSAREQGLHFYAAGHHATERGGIRALSEWLNENTDLDVTFIDIPNPA

Source Source

Source organism organism	Escherichia coli, Escherichia coli O157:H7
Common name common_name	,
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	576

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1nmpa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
Superfamily Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
Family Family family	c.135.1.1 — NIF3 (NGG1p interacting factor 3)-like

Domain ID domain_id	d1nmpb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
Superfamily Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
Family Family family	c.135.1.1 — NIF3 (NGG1p interacting factor 3)-like

Domain ID domain_id	d1nmpc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
Superfamily Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
Family Family family	c.135.1.1 — NIF3 (NGG1p interacting factor 3)-like

Domain ID domain_id	d1nmpd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
Superfamily Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
Family Family family	c.135.1.1 — NIF3 (NGG1p interacting factor 3)-like

Domain ID domain_id	d1nmpe_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
Superfamily Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
Family Family family	c.135.1.1 — NIF3 (NGG1p interacting factor 3)-like

Domain ID domain_id	d1nmpf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
Superfamily Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
Family Family family	c.135.1.1 — NIF3 (NGG1p interacting factor 3)-like

CATH v4.4 (12 domains)

Domain ID domain_id	1nmpA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

Domain ID domain_id	1nmpA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

Domain ID domain_id	1nmpB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

Domain ID domain_id	1nmpB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

Domain ID domain_id	1nmpC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

Domain ID domain_id	1nmpC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

Domain ID domain_id	1nmpD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

Domain ID domain_id	1nmpD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

Domain ID domain_id	1nmpE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

Domain ID domain_id	1nmpE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

Domain ID domain_id	1nmpF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

Domain ID domain_id	1nmpF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

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Unit-cell length a length_a	156.730 Å
Unit-cell length b length_b	156.730 Å
Unit-cell length c length_c	57.610 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	P 3
Space-group number int_tables_number	143
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	19.760 Å
R factor r_factor	0.2120
R_work r_work	0.2120
R_free r_free	0.2530

Structural genomics, ybgI protein, unknown function

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

Hypothetical protein ybgI

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

1nmp__assembly_4__model_1

1nmp__assembly_4__model_1 | I(q)

1nmp__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) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Structural genomics, ybgI protein, unknown function

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

Hypothetical protein ybgI

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

1nmp__assembly_4__model_1

1nmp__assembly_4__model_1 | I(q)

1nmp__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) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)