SAXSdb — 1be4

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

NUCLEOSIDE DIPHOSPHATE TRANSFERASE

Bos taurus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–151 Chain B； UniProt 1–151 Chain C； UniProt 1–151	Not recorded	PCG CYCLIC GUANOSINE MONOPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7	Resolution 2.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	NDKB_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–151； UniProt 1–151 Author chain B； PDBConstruct 1–151； UniProt 1–151 Author chain C； PDBConstruct 1–151； UniProt 1–151

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	1be4
Deposition date deposition_date	1998-05-19
Structure title title	NUCLEOSIDE DIPHOSPHATE KINASE ISOFORM B FROM BOVINE RETINA
Keywords keywords	PHOSPHOTRANSFERASE; PHOSPHOTRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.15 Å
Radius of gyration Rg (electron density) rg_electron	24.46 Å
Forward intensity I(0) i0	46335100.00
Molecular weight molecular_weight	52539.0 kDa
Excluded volume excluded_volume	65658 Å³
Envelope volume envelope_volume	76438 Å³
Hydration-shell volume shell_volume	26141 Å³
Envelope diameter envelope_diameter	80.0 Å
Shell Rg shell_rg	31.43 Å
Envelope Rg envelope_rg	24.56 Å
Shape Rg shape_rg	24.48 Å
Total Rg total_rg	25.17 Å
Total atoms total_atoms	3690
Residues n_residues	453
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	77.2 Å
Rg (real space) rg_real	25.10 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	4.6340e+07
I(0) uncertainty (real space) i0_real_error	5.9870e+05
Rg (reciprocal space) rg_reciprocal	25.12 Å
I(0) (reciprocal space) i0_reciprocal	46340000.0000
Solution quality estimate total_estimate	0.9113
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.8 Å
Skewness Skewness skewness	0.208
Kurtosis Kurtosis kurtosis	-0.662
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	30000000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.966

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	NUCLEOSIDE DIPHOSPHATE TRANSFERASE
Molecular weight formula_weight	17190.8 kDa
EC 编号 ec_number	2.7.4.6
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	3968

ANSERTFIAIKPDGVQRGLMGEIIKRFEQKGFRLVAMKFMRASEDLLKEHYIDLKDRPFFAGLVKYMHSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVESAEKEIALWFRPEELVNYKSCAQNWIYE

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	cattle
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CYCLIC GUANOSINE MONOPHOSPHATE
Molecular weight formula_weight	345.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	278

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1be4a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.6 — Nucleoside diphosphate kinase, NDK
Family Family family	d.58.6.1 — Nucleoside diphosphate kinase, NDK

Domain ID domain_id	d1be4b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.6 — Nucleoside diphosphate kinase, NDK
Family Family family	d.58.6.1 — Nucleoside diphosphate kinase, NDK

Domain ID domain_id	d1be4c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.6 — Nucleoside diphosphate kinase, NDK
Family Family family	d.58.6.1 — Nucleoside diphosphate kinase, NDK

CATH v4.4 (3 domains)

Domain ID domain_id	1be4A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	141 — Nucleoside diphosphate kinase-like domain

Domain ID domain_id	1be4B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	141 — Nucleoside diphosphate kinase-like domain

Domain ID domain_id	1be4C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	141 — Nucleoside diphosphate kinase-like domain

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8. Citations (1)

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Unit-cell length a length_a	128.610 Å
Unit-cell length b length_b	128.610 Å
Unit-cell length c length_c	88.180 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	24

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/be/1be4/1be4.fit
pddf	/app/data/pr_computation/be/1be4/1be4.pr.out
profile	/app/data/saxs_computation/be/1be4/1be4.dat

NUCLEOSIDE DIPHOSPHATE KINASE ISOFORM B FROM BOVINE RETINA

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

NUCLEOSIDE DIPHOSPHATE TRANSFERASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction