3bid

Crystal structure of the NMB1088 protein from Neisseria meningitidis. Northeast Structural Genomics Consortium target MR91

Method: X-RAY DIFFRACTION

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

UPF0339 protein NMB1088

Neisseria meningitidis MC58

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 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y1088_NEIMB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–56； UniProt 1–56 Author chain B； PDBConstruct 1–56； UniProt 1–56 Author chain C； PDBConstruct 1–56； UniProt 1–56 Author chain D； PDBConstruct 1–56； UniProt 1–56 Author chain E； PDBConstruct 1–56； UniProt 1–56 Author chain F； PDBConstruct 1–56； UniProt 1–56 Author chain G； PDBConstruct 1–56； UniProt 1–56 Author chain H； PDBConstruct 1–56； UniProt 1–56

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	3bid
Deposition date deposition_date	2007-11-30
Structure title title	Crystal structure of the NMB1088 protein from Neisseria meningitidis. Northeast Structural Genomics Consortium target MR91
Keywords keywords	;alpha-beta protein, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, 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.

3bid__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3bid__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bid__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	15.99 Å
Rg (electron density)	14.81 Å
Total Rg	15.85 Å
Atom count	964
Residues	117
Excluded volume	17067 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bid__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3bid__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3bid__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3bid__assembly_4__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 (2)

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d3bida1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.348 — YegP-like
Superfamily Superfamily superfamily	d.348.1 — YegP-like
Family Family family	d.348.1.1 — YegP-like

Domain ID domain_id	d3bida2
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	d3bidb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.348 — YegP-like
Superfamily Superfamily superfamily	d.348.1 — YegP-like
Family Family family	d.348.1.1 — YegP-like

Domain ID domain_id	d3bidb3
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	d3bidc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.348 — YegP-like
Superfamily Superfamily superfamily	d.348.1 — YegP-like
Family Family family	d.348.1.1 — YegP-like

Domain ID domain_id	d3bidc3
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	d3bidd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.348 — YegP-like
Superfamily Superfamily superfamily	d.348.1 — YegP-like
Family Family family	d.348.1.1 — YegP-like

Domain ID domain_id	d3bidd3
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	d3bide2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.348 — YegP-like
Superfamily Superfamily superfamily	d.348.1 — YegP-like
Family Family family	d.348.1.1 — YegP-like

Domain ID domain_id	d3bide3
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	d3bidf2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.348 — YegP-like
Superfamily Superfamily superfamily	d.348.1 — YegP-like
Family Family family	d.348.1.1 — YegP-like

Domain ID domain_id	d3bidf3
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	d3bidg2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.348 — YegP-like
Superfamily Superfamily superfamily	d.348.1 — YegP-like
Family Family family	d.348.1.1 — YegP-like

Domain ID domain_id	d3bidg3
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	d3bidh2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.348 — YegP-like
Superfamily Superfamily superfamily	d.348.1 — YegP-like
Family Family family	d.348.1.1 — YegP-like

Domain ID domain_id	d3bidh3
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 (8 domains)

Domain ID domain_id	3bidA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	160 — YegP-like

Domain ID domain_id	3bidB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	160 — YegP-like

Domain ID domain_id	3bidC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	160 — YegP-like

Domain ID domain_id	3bidD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	160 — YegP-like

Domain ID domain_id	3bidE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	160 — YegP-like

Domain ID domain_id	3bidF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	160 — YegP-like

Domain ID domain_id	3bidG01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	160 — YegP-like

Domain ID domain_id	3bidH01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	160 — YegP-like

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Unit-cell length a length_a	34.743 Å
Unit-cell length b length_b	60.040 Å
Unit-cell length c length_c	64.370 Å
Unit-cell angle α angle_alpha	89.39 °
Unit-cell angle β angle_beta	90.81 °
Unit-cell angle γ angle_gamma	103.97 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	19.810 Å
R factor r_factor	0.2410
R_work r_work	0.2410
R_free r_free	0.2900

Description description	UPF0339 protein NMB1088
Molecular weight formula_weight	7531.3 kDa
Source method src_method	man
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	3787

Crystal structure of the NMB1088 protein from Neisseria meningitidis. Northeast Structural Genomics Consortium target MR91

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

UPF0339 protein NMB1088

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

3bid__assembly_3__model_1

3bid__assembly_3__model_1 | I(q)

3bid__assembly_3__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) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Source organism organism	Neisseria meningitidis MC58
NCBI taxonomy ID ncbi_taxonomy_id	122586
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	28

Crystal structure of the NMB1088 protein from Neisseria meningitidis. Northeast Structural Genomics Consortium target MR91

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

UPF0339 protein NMB1088

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

3bid__assembly_3__model_1

3bid__assembly_3__model_1 | I(q)

3bid__assembly_3__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) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. Citations (1)