SAXSdb — 3gvj

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

Endo-N-acetylneuraminidase

Enterobacteria phage K1F

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 3 其他Polymer 6	;N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-beta-neuraminic acid ; × 3 ;N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-beta-neuraminic acid ; × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q858B1_BPK1F
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–670； UniProt 246–910

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	3gvj
Deposition date deposition_date	2009-03-31
Structure title title	Crystal structure of an endo-neuraminidaseNF mutant
Keywords keywords	endo-Neuraminidase; polySialic acid; triple-beta helix, Glycosidase, Hydrolase; HYDROLASE
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.

3gvj__assembly_1__model_1

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

Download this curve (.dat)

3gvj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gvj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.19 Å
Rg (electron density)	38.34 Å
Total Rg	38.85 Å
Atom count	16305
Residues	2010
Excluded volume	285380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gvj__assembly_1__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	Endo-N-acetylneuraminidase
Molecular weight formula_weight	74456.3 kDa
EC 编号 ec_number	3.2.1.129
Mutation mutation	R647A
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	6457

VPRGSAKGDGVTDDTAALTSALNDTPVGQKINGNGKTYKVTSLPDISRFINTRFVYERIPGQPLYYASEEFVQGELFKITDTPYYNAWPQDKAFVYENVIYAPYMGSDRHGVSRLHVSWVKSGDDGQTWSTPEWLTDLHPDYPTVNYHCMSMGVCRNRLFAMIETRTLAKNALTNCALWDRPMSRSLHLTGGITKAANQRYATIHVPDHGLFVGDFVNFSNSAVTGVSGDMTVATVIDKDNFTVLTPNQQTSDLNNAGKNWHMGTSFHKSPWRKTDLGLIPSVTEVHSFATIDNNGFAMGYHQGDVAPREVGLFYFPDAFNSPSNYVRRQIPSEYEPDASEPCIKYYDGVLYLITRGTRGDRLGSSLHRSRDIGQTWESLRFPHNVHHTTLPFAKVGDDLIMFGSEAAENEWEAGAPDDRYKASYPRTFYARLNVNNWNADDIEWVNITDQIYQGGIVNSGVGVGSVVVKDNYIYYMFGGEDHFNPWTYGDNSAKDPFKSDGHPSDLYCYKMKIGPDNRVSRDFRYGAVPNRAVPVFFDTNGVRTVPAPMEFTGDLGLGHVTIRASTSSNIRSEVLMEGEYGFIGKSIPTDNPAGQRIIFCGGEGTSSTTGAQITLYGANNTDSRRIVYNGDEHLFQSADVKPYNDNVTALGGPSNRFTTAYLGSNPIVT

Source Source

Source organism organism	Enterobacteria phage K1F
Common name common_name	Bacteriophage K1F
NCBI taxonomy ID ncbi_taxonomy_id	344021
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	;N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-beta-neuraminic acid ;
Molecular weight formula_weight	1474.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 branched

Description description	;N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-beta-neuraminic acid ;
Molecular weight formula_weight	1183.0 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	850

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3gvja1
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.1 — Sialidases
Family Family family	b.68.1.2 — Endo-alpha-sialidase

Domain ID domain_id	d3gvja2
Class class	b — All beta proteins
Fold Fold fold	b.108 — Triple-stranded beta-helix
Superfamily Superfamily superfamily	b.108.1 — Phage fibre proteins
Family Family family	b.108.1.0 — automated matches

Domain ID domain_id	d3gvja3
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 (4 domains)

Domain ID domain_id	3gvjA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	750 — Transcription Regulator spoIIAA
Homologous superfamily homologous superfamily	60 — Endosialidase, N-terminal extension domain

Domain ID domain_id	3gvjA02
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3gvjA03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3gvjA04
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1090 — Endosialidase, domain 4
Homologous superfamily homologous superfamily	10 — Endosialidase, domain 4

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Unit-cell length a length_a	119.090 Å
Unit-cell length b length_b	119.090 Å
Unit-cell length c length_c	175.980 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	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.480 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	0.1951
R_work r_work	0.1940
R_free r_free	0.2164

Crystal structure of an endo-neuraminidaseNF mutant

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

Endo-N-acetylneuraminidase

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

3gvj__assembly_1__model_1

3gvj__assembly_1__model_1 | I(q)

3gvj__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of an endo-neuraminidaseNF mutant

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

Endo-N-acetylneuraminidase

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

3gvj__assembly_1__model_1

3gvj__assembly_1__model_1 | I(q)

3gvj__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)