SAXSdb — 2gkp

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

hypothetical protein NMB0488

Neisseria meningitidis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SODIUM ION × 1 1,2-ETHANEDIOL × 1 BETA-MERCAPTOETHANOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9K0T5_NEIMB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–167； UniProt 1–164

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	2gkp
Deposition date deposition_date	2006-04-03
Structure title title	Protein of Unknown Function NMB0488 from Neisseria meningitidis
Keywords keywords	;structural genomics, APC83854, hypothetical protein, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, 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.

2gkp__assembly_1__model_1

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

Download this curve (.dat)

2gkp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2gkp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.92 Å
Rg (electron density)	15.67 Å
Total Rg	16.75 Å
Atom count	1338
Residues	161
Excluded volume	23719 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2gkp__assembly_1__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	hypothetical protein NMB0488
Molecular weight formula_weight	19279.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1847

SNAMTFNQEQDYWAGYKANERALIIQTWSGFGRYAPDHLYPPHILPLDTDNETLGTTVLQALANSRTFVYDSPEDQDFFDTEKIRQRYEDWVAKLCGNLGYKTRRALFKNMMSVDIWLHNGCLKISPSRHVKLEAWDAIDADDVILSLDNSPEEIGAGLKLALSRCR

Source Source

Source organism organism	Neisseria meningitidis
NCBI taxonomy ID ncbi_taxonomy_id	122586
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	392

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2gkpa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.351 — NMB0488-like
Superfamily Superfamily superfamily	d.351.1 — NMB0488-like
Family Family family	d.351.1.1 — NMB0488-like

CATH v4.4 (1 domains)

Domain ID domain_id	2gkpA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1590 — NMB0488-like fold
Homologous superfamily homologous superfamily	10 — NMB0488-like

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Unit-cell length a length_a	48.102 Å
Unit-cell length b length_b	79.877 Å
Unit-cell length c length_c	44.624 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.350 Å
Low-resolution limit resolution_low	30.400 Å
R factor r_factor	0.1536
R_work r_work	0.1541
R_free r_free	0.2065

Protein of Unknown Function NMB0488 from Neisseria meningitidis

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

hypothetical protein NMB0488

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

2gkp__assembly_1__model_1

2gkp__assembly_1__model_1 | I(q)

2gkp__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Protein of Unknown Function NMB0488 from Neisseria meningitidis

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

hypothetical protein NMB0488

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

2gkp__assembly_1__model_1

2gkp__assembly_1__model_1 | I(q)

2gkp__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)