3gvk

Crystal structure of endo-neuraminidase NF mutant

Method: X-RAY DIFFRACTION

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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 9	N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-beta-neuraminic acid × 6 N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-beta-neuraminic acid × 3 SODIUM ION × 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 Author chain B； PDBConstruct 6–670； UniProt 246–910 Author chain C； 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	3gvk
Deposition date deposition_date	2009-03-31
Structure title title	Crystal structure of endo-neuraminidase NF 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.

3gvk__assembly_1__model_1

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

Download this curve (.dat)

3gvk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gvk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.05 Å
Rg (electron density)	38.19 Å
Total Rg	38.68 Å
Atom count	16020
Residues	1976
Excluded volume	280560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gvk__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 (5)

Entity 1 Entity 1 polymer

Description description	Endo-N-acetylneuraminidase
Molecular weight formula_weight	74475.4 kDa
EC 编号 ec_number	3.2.1.129
Mutation mutation	H350A
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	18367

VPRGSAKGDGVTDDTAALTSALNDTPVGQKINGNGKTYKVTSLPDISRFINTRFVYERIPGQPLYYASEEFVQGELFKITDTPYYNAWPQDKAFVYENVIYAPYMGSDRAGVSRLHVSWVKSGDDGQTWSTPEWLTDLHPDYPTVNYHCMSMGVCRNRLFAMIETRTLAKNALTNCALWDRPMSRSLHLTGGITKAANQRYATIHVPDHGLFVGDFVNFSNSAVTGVSGDMTVATVIDKDNFTVLTPNQQTSDLNNAGKNWHMGTSFHKSPWRKTDLGLIPSVTEVHSFATIDNNGFAMGYHQGDVAPREVGLFYFPDAFNSPSNYVRRQIPSEYEPDASEPCIKYYDGVLYLITRGTRGDRLGSSLHRSRDIGQTWESLRFPHNVHHTTLPFAKVGDDLIMFGSERAENEWEAGAPDDRYKASYPRTFYARLNVNNWNADDIEWVNITDQIYQGGIVNSGVGVGSVVVKDNYIYYMFGGEDHFNPWTYGDNSAKDPFKSDGHPSDLYCYKMKIGPDNRVSRDFRYGAVPNRAVPVFFDTNGVRTVPAPMEFTGDLGLGHVTIRASTSSNIRSEVLMEGEYGFIGKSIPTDNPAGQRIIFCGGEGTSSTTGAQITLYGANNTDSRRIVYNGDEHLFQSADVKPYNDNVTALGGPSNRFTTAYLGSNPIVT

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-beta-neuraminic acid
Molecular weight formula_weight	891.8 kDa
Source method src_method	man
Copy count entity_count	6

Entity 3 Entity 3 branched

Description description	N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-beta-neuraminic acid
Molecular weight formula_weight	600.5 kDa
Source method src_method	man
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2130

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3gvka1
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	d3gvka2
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	d3gvkb1
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	d3gvkb2
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	d3gvkb3
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	d3gvkc1
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	d3gvkc2
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	d3gvkc3
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 (12 domains)

Domain ID domain_id	3gvkA01
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	3gvkA02
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3gvkA03
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	3gvkA04
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1090 — Endosialidase, domain 4
Homologous superfamily homologous superfamily	10 — Endosialidase, domain 4

Domain ID domain_id	3gvkB01
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	3gvkB02
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3gvkB03
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	3gvkB04
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1090 — Endosialidase, domain 4
Homologous superfamily homologous superfamily	10 — Endosialidase, domain 4

Domain ID domain_id	3gvkC01
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	3gvkC02
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3gvkC03
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	3gvkC04
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	90.400 Å
Unit-cell length b length_b	153.700 Å
Unit-cell length c length_c	157.800 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.840 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2657
R_work r_work	0.2648
R_free r_free	0.2823

Crystal structure of endo-neuraminidase NF 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

3gvk__assembly_1__model_1

3gvk__assembly_1__model_1 | I(q)

3gvk__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 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of endo-neuraminidase NF 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

3gvk__assembly_1__model_1

3gvk__assembly_1__model_1 | I(q)

3gvk__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 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)